Gut microbiota and neurodevelopement analysis

Part 1: Data description

Outcomes

Table 1: Neurodeveloppement variables description

Variable labels	Min	Q1	Median	Mean	Q3	Max	N	W_statistic_shapiro	p_value_shapiro
Child interne score at 2 years (CBCL)	0	3	6	6.9	9	29	417	0.9	<0.001
Child externe score at 2 years (CBCL)	1	9	12	13.2	17	37	416	1	<0.001
Child social awareness score at 3 years (SRS)	0	4	5	5.6	7	15	407	1	<0.001
Child social cognition score at 3 years (SRS)	0	3	5	5.2	7	15	407	1	<0.001
Child social communication score at 3 years (SRS)	0	5	8	8.6	11	39	407	0.9	<0.001
Child social motivation score at 3 years (SRS)	0	3	5	5.9	8	21	407	0.9	<0.001
Child restricted interests and repetitive behavior score at 3 years (SRS)	0	1	3	3.6	5	18	407	0.9	<0.001
Child SRS total score at 3 years (SRS)	4	20	26	28.9	36	100	407	0.9	<0.001
Child inhibition score at 3 years (BRIEF-P)	16	20	24	23.9	27	45	405	1	<0.001
Child shift score at 3 years (BRIEF-P)	10	11	13	13.3	15	28	414	0.9	<0.001
Child emotional control score at 3 years (BRIEF-P)	10	12	14	14.8	17	29	414	0.9	<0.001
Child working memory score at 3 years (BRIEF-P)	17	18	21	21.6	24	43	406	0.9	<0.001
Child plan/organization score at 3 years (BRIEF-P)	10	12	14	14.1	16	25	411	1	<0.001
Verbal comprehension score at 3 years (IQ test)	81	104	113	113.0	120	144	381	1	<0.001
Visuospatiale score at 3 years (IQ test)	82	100	106	107.6	115	135	382	1	1.537864e-03
Work memory score at 3 years (IQ test)	75	100	106	106.3	112	146	380	1	1.486267e-02
Total IQ score at 3 years	83	103	110	111.4	118	145	381	1	9.672147e-03

Figure 1: Spearman correlations between neurodeveloppment variables

CBCL Y2

Interne score Y2

Figure 2: Distribution of CBCL interne score Y2 (n = 417)

Outliers values of child interne score at 2 years variable (CBCL)

ident	ch_cbclintscore_y2
27630	19
28199	19
15218	20
17764	20
25913	20
22672	21
23696	21
24222	22
16786	24
27316	25
15713	26
15804	29

Externe score Y2

Figure 3: Distribution of CBCL externe score Y2 (n = 416)

ident	ch_cbclextscore_y2
19494	30
14567	32
16786	34
15218	35
16088	37

SRS Y3

Social awareness score Y3

Figure 4: Distribution of social awareness score Y3 (SRS, n = 407)

Outliers values of child social awareness score at 3 years (SRS) variable

ident	ch_socawar_y3
14986	12
16088	12
17886	12
18868	12
21185	12
21519	12
23250	12
26318	12
22042	13
25823	13
15218	15

Social cognition score Y3

Figure 5: Distribution of social cognition score Y3 (SRS, n = 407)

Outliers values of child social cognition score at 3 years (SRS) variable

ident	ch_soccog_y3
16318	14
16407	14
19029	14
26952	14
23663	15
24226	15
26318	15

Social communication score at 3 years

Figure 6: Distribution of social communication score at 3 years (SRS, n = 407)

Outliers values of child social communication score at 3 years (SRS) variable

ident	ch_soccom_y3
17668	21
24226	21
19677	22
22042	22
23805	22
16093	24
23696	25
26952	27
15218	39

Social motivation score Y3

Figure 7: Distribution of social motivation score Y3 (SRS, n = 407)

Outliers values of child social motivation score at 3 years (SRS) variable

ident	ch_socmot_y3
15218	16
19029	16
24476	16
17524	17
23603	17
23020	18
14276	19
26952	19
15804	21

Restricted interests and repetitive behavior score Y3

Figure 8: Distribution of restricted interests and repetitive behavior score Y3 (SRS, n = 407)

Outliers values of child restricted interests and repetitive behavior score at 3 years (SRS) variable

ident	ch_RRB_y3
14856	12
16088	12
17764	12
26952	12
22167	13
15821	14
25409	15
15218	18

SRS total score at 3 years

Figure 9: Distribution of SRS total score at 3 years (SRS, n = 407)

Outliers values of child SRS total score at 3 years (SRS) variable

ident	ch_SRStotal_y3
19677	62
23696	62
24226	65
16093	70
26952	80
15218	100

BRIEF-P Y3

Inhibition score Y3

Figure 10: Distribution of inhibition score Y3 (BRIEF-P, n = 405)

Outliers values of child inhibition score at 3 years (BRIEF-P) variable

ident	ch_briefpinhibit_y3
19418	38
19426	39
24226	39
15821	40
18868	40
16021	43
15218	44
16088	45

Shift score Y3

Figure 11: Distribution of shift score Y3 (BRIEF-P, n = 414)

Outliers values of child shift score at 3 years (BRIEF-P) variable

ident	ch_briefpshift_y3
27316	22
15741	23
15804	26
14276	28

Emotional control score Y3

Figure 12: Distribution of emotional control score Y3 (BRIEF-P, n = 414)

Outliers values of child emotional control score at 3 years (BRIEF-P) variable

ident	ch_briefpemocontrol_y3
15741	25
22992	25
24222	25
16088	27
16021	28
19426	28
25409	28
15218	29

Working memory score Y3

Figure 13: Distribution of working memory score Y3 (BRIEF-P, n = 406)

Outliers values of child working memory score at 3 years (BRIEF-P) variable

ident	ch_briefpworkmemo_y3
27309	34
19418	37
24226	41
16088	43

Plan/organization score Y3

Figure 14: Distribution of plan/organization score Y3 (BRIEF-P, n = 411)

Outliers values of child plan/organization score at 3 years (BRIEF-P) variable

ident	ch_briefpplan_y3
16088	25

IQ Y3

Verbal comprehension score Y3

Figure 15: Distribution of verbal comprehension score Y3 (IQ, n = 381)

Verbal comprehension score Y3 variable doesn’t have any outliers.

Visuospatiale score Y3

Figure 16: Distribution of visuospatiale score Y3 (IQ, n = 382)

Visuospatiale score at 3 years (IQ test) doesn’t have any outliers.

Work memory score Y3

Figure 17: Distribution of work memory score Y3 (IQ, n = 380)

Outliers values of work memory score at 3 years (IQ test) variable

ident	ch_work_memory_IQ_Y3
28226	75
25269	78
25784	78
24374	79
14856	80
17496	134
22857	134
27891	134
23769	146

Total IQ score Y3

Figure 18: Distribution of total IQ score Y3 (IQ, n = 381)

Outliers values of total IQ score at 3 years variable

ident	ch_total_IQ_Y3
26097	145
28047	145

Predictors

Table 2: Gut microbiota variables description at one year

Variable labels	Min	Q1	Median	Mean	Q3	Max	N	W_statistic_shapiro	p_value_shapiro
Specific richness diversity in 1Y child gut microbiota ASV based (seq. depth = 5 000)	18	64	81	83.2	99	184	350	1	1.429062e-03
Shannon diversity in 1Y child gut microbiota ASV based (seq. depth = 5 000)	0	2	3	2.6	3	4	350	1	<0.001
Faith diversity in 1Y child gut microbiota ASV based (seq. depth = 5 000)	86	266	311	314.5	362	560	350	1	6.345057e-01
One year child feces relative abundance of phylum Firmicutes	1	22	36	38.1	51	91	356	1	<0.001
One year child feces relative abundance of phylum Actinobacteria	0	11	26	30.0	48	98	356	0.9	<0.001
One year child feces relative abundance of phylum Bacteroidetes	0	3	10	17.4	28	80	356	0.9	<0.001
One year child feces relative abundance of phylum Proteobacteria	0	0	2	8.3	7	93	356	0.6	<0.001
One year child feces relative abundance of genus Bifidobacterium	0	10	25	29.0	46	98	356	0.9	<0.001
One year child feces relative abundance of genus Bacteroides	0	2	9	15.6	26	78	356	0.8	<0.001
One year child feces relative abundance of genus Blautia	0	1	4	8.2	11	68	356	0.8	<0.001
One year child feces relative abundance of genus Escherichia_Shigella	0	0	1	6.6	5	93	356	0.5	<0.001

Table 3: Gut microbiota variables description at one year (log transformed)

Variable labels	Min	Q1	Median	Mean	Q3	Max	N
One year child feces relative abundance of phylum Firmicutes	0	3	4	3.5	4	5	356
One year child feces relative abundance of phylum Actinobacteria	-4	2	3	2.9	4	5	356
One year child feces relative abundance of phylum Bacteroidetes	-Inf	1	2	-Inf	3	4	356
One year child feces relative abundance of phylum Proteobacteria	-Inf	-1	0	-Inf	2	5	356
One year child feces relative abundance of genus Bifidobacterium	-4	2	3	2.8	4	5	356
One year child feces relative abundance of genus Bacteroides	-Inf	1	2	-Inf	3	4	356
One year child feces relative abundance of genus Blautia	-Inf	0	1	-Inf	2	4	356
One year child feces relative abundance of genus Escherichia_Shigella	-Inf	-2	0	-Inf	2	5	356

Table 4: visualization of -inf values after log transformation

ident	ch_feces_rel_p3_Y1_ln	ch_feces_rel_p4_Y1_ln	ch_feces_rel_g2_Y1_ln	ch_feces_rel_g3_Y1_ln	ch_feces_rel_g4_Y1_ln
14173	4.0013507	3.76118491	4.0013507	-Inf	3.7330816
14979	3.2473059	-1.70675905	-3.4295257	-Inf	-1.9944411
16115	-1.8336282	-1.79791010	-2.0342989	-Inf	-1.7979101
16199	3.9841257	2.41167366	3.9841257	-Inf	2.4087316
16815	-2.4944719	1.59987269	-Inf	2.94621274	1.5998727
17095	2.0352511	-0.03902244	1.5745307	3.10049773	-Inf
17537	-0.3474013	-2.62466859	-0.6787584	-Inf	-2.6246686
17700	-3.0402275	3.69019375	-3.0402275	-Inf	3.6848061
17741	1.8447974	0.36339523	1.8441227	-Inf	-0.6125006
18673	-3.8495800	-2.30913502	-3.8495800	-2.55029708	-Inf
20640	2.3160464	0.72944149	2.2843500	3.55481991	-Inf
21511	3.6167621	3.85946829	3.6167621	-Inf	3.8518964
21967	2.9506783	0.16107821	2.7535488	1.85055883	-Inf
22059	0.8230470	4.02241500	-Inf	0.79290287	0.7553010
22368	4.1303734	1.78002318	3.8239975	-Inf	1.0516510
22809	-Inf	2.11185197	-Inf	0.06626866	2.0967944
23076	4.0280313	3.05793567	4.0280313	-Inf	3.0174951
23271	-Inf	3.63094162	-Inf	0.97573630	3.6275579
23327	-1.6907665	-Inf	-1.6907665	1.52446633	-Inf
23769	-Inf	3.97694943	-Inf	-Inf	2.8884448
23933	1.3343488	1.29793974	1.3343488	-Inf	0.7797483
25166	-0.9454993	-0.67434655	-1.4187870	3.17872231	-Inf
25344	3.5488133	1.90877329	3.5488133	-Inf	1.9080366
25913	2.2533679	1.59834855	2.1940970	2.17730336	-Inf
26457	-0.5737519	-0.77346516	-0.5911436	3.40043617	-Inf
27344	3.7990176	-0.97953604	3.7961633	0.75406751	-Inf
27490	0.2535176	3.76993665	0.2535176	-Inf	3.7233742

Figure 19: Spearman correlations between gut microbiota variables (n=350)

Alpha diversity

Specific richness

Figure 20: Distribution of the specific richness Y1 (n=350)

Outliers values of Specific richness variable

ident	ch_feces_SpecRich_5000_ASV_Y1
27075	154
24255	158
23901	184

Shannon diversity

Figure 21: Distribution of the Shannon diversity Y1 (n=350)

Outliers values of Shannon diversity variable

ident	ch_feces_Shannon_5000_ASV_Y1
23330	0.3792690
28130	0.9867788
16115	1.0087967
24587	1.0558328
18553	1.0624003
22720	1.1855234
14173	1.2115941

Faith’s phylogenetic diversity

Figure 22: Distribution of the Faith’s phylogenetic diversity Y1 (n=350)

Outliers values of Faith's phylogenetic diversity variable

ident	ch_feces_Faith_5000_ASV_Y1
23769	85.94050
23330	93.96517
22720	106.85055
18440	505.49615
24255	521.84691
23901	559.55928

Taxonomy

Phylum Firmicutes relative abundance Y1

Figure 23: Distribution of the relative abundance of phylum Firmicutes Y1 (n=356)

Phylum Firmicutes variable at one year doesn’t have any outliers.

Phylum Actinobacteria Y1

Figure 24: Distribution of the relative abundance of phylum Actinobacteria Y1 (n=356)

Phylum Actinobacteria variable at one year doesn’t have any outliers.

Phylum Bacteroidetes Y1

Figure 25: Distribution of the relative abundance of phylum Bacteroidetes Y1 (n=356)

Outliers values of phylum Bacteroidetes variable

ident	ch_feces_rel_p3_Y1
22198	70.99179
16606	76.94366
16650	78.31132
24006	78.76686
14856	80.30181

Figure 26: Distribution of the relative abundance of ln(phylum Bacteroidetes) Y1 (n=356)

Outliers values of phylum Bacteroidetes variable (ln)

ident	ch_feces_rel_p3_Y1_ln
22809	-Inf
23271	-Inf
23769	-Inf
16294	-4.843215
23663	-4.822537
19261	-4.776515
26766	-4.058314
28130	-3.990227
24359	-3.986871
25943	-3.902646
24226	-3.878053
18673	-3.849580
25673	-3.757706
15645	-3.562371
21955	-3.457762
22094	-3.436857
16782	-3.434826
18002	-3.417399
22857	-3.289927
16546	-3.252476
26760	-3.223505
17673	-3.041327
17700	-3.040228
22812	-2.922557
15422	-2.893700
22126	-2.655846
23848	-2.624384

Phylum Proteobacteria Y1

Figure 27: Distribution of the relative abundance of phylum Proteobacteria Y1 (n=356)

Outliers values of phylum Proteobacteria variable

ident	ch_feces_rel_p4_Y1
22992	17.43845
16403	17.50454
20151	18.00766
16766	18.42998
15066	18.55562
21048	19.64709
20194	19.73358
22167	20.55545
23603	21.24552
23076	21.28358
26806	22.15355
25433	22.87679
16958	24.66083
27658	24.67874
15567	24.82301
27706	24.94526
15741	25.67847
21785	25.85059
25784	26.10054
27747	27.90090
18501	28.26770
15422	28.44487
26882	29.20354
19261	30.38588
23816	30.99024
17664	35.91379
25668	36.53393
22640	37.17140
23271	37.74834
21839	37.90993
16435	39.13336
17700	40.05261
14173	42.99935
27490	43.37732
22364	44.71383
23275	45.57840
21511	47.44012
25943	52.63795
23769	53.35403
27305	53.50392
22059	55.83579
26750	59.01700
27002	59.23331
17673	59.81226
27023	62.53976
27954	62.99872
15768	64.65962
20502	66.62831
26237	67.07950
20386	67.93516
27968	71.50482
28226	71.58796
28130	74.46033
23330	93.31640

Figure 28: Distribution of the relative abundance of ln(phylum Proteobacteria) Y1 (n=356)

Outliers values of phylum Proteobacteria variable (ln)

ident	ch_feces_rel_p4_Y1_ln
23327	-Inf
17617	-5.459735
16682	-5.270843

Genus Bifidobacterium Y1

Figure 29: Distribution of the relative abundance of genus Bifidobacterium Y1 (n=356)

Genus Bifidobacterium variable at one year doesn’t have any outliers.

Genus Bacteroides Y1

Figure 30: Distribution of the relative abundance of genus Bacteroides Y1 (n=356)

Outliers values of genus Bacteroides variable

ident	ch_feces_rel_g2_Y1
25773	63.55170
22198	64.72573
22772	65.80880
16606	68.58547
16650	74.61496
14856	77.49379
24006	77.75224

Figure 31: Distribution of the relative abundance of ln(genus Bacteroides) Y1 (n=356)

Outliers values of genus Bacteroides variable (ln)

ident	ch_feces_rel_g2_Y1_ln
16815	-Inf
22059	-Inf
22809	-Inf
23271	-Inf
23769	-Inf
17365	-6.318373
19261	-5.469662
26318	-5.402362
23848	-5.263441
20194	-5.230699
16294	-4.843215
28130	-4.837525
23663	-4.822537
25501	-4.633932
24954	-4.556295
22620	-4.532277
16782	-4.351116
25943	-4.308111
26606	-4.245873
22640	-4.230137
22857	-4.078385
26766	-4.058314
24359	-3.986871
24226	-3.878053
18673	-3.849580
20110	-3.772958
25673	-3.757706
18002	-3.618069
15645	-3.562371
22094	-3.532167
21955	-3.457762

Genus Blautia Y1

Figure 32: Distribution of the relative abundance of genus Blautia Y1 (n=356)

Outliers values of genus Blautia variable

ident	ch_feces_rel_g3_Y1
24359	26.88639
26606	26.94677
26743	27.03046
24862	27.17326
16766	27.40951
22757	29.04340
23603	29.09020
17617	29.59134
26457	29.97717
24995	30.53021
18664	30.65735
18509	32.11204
18199	32.12291
17524	32.23506
27058	32.59997
14177	32.92643
20640	34.98152
22118	35.07580
27526	35.50186
24917	35.57943
27854	35.87615
15186	36.93569
25281	40.66080
19367	40.80985
22812	44.02528
16546	67.83070

Figure 33: Distribution of the relative abundance of ln(genus Blautia) Y1 (n=356)

Outliers values of genus Blautia variable (ln)

ident	ch_feces_rel_g3_Y1_ln
14173	-Inf
14979	-Inf
16115	-Inf
16199	-Inf
17537	-Inf
17700	-Inf
17741	-Inf
21511	-Inf
22368	-Inf
23076	-Inf
23769	-Inf
23933	-Inf
25344	-Inf
27490	-Inf
15567	-5.890539
22720	-5.783764
18780	-5.716732
25773	-5.658367
27309	-5.314486
18002	-5.122147
28199	-5.051393
25416	-5.044199
23330	-5.033766
25943	-5.001258
19995	-4.977469
19261	-4.371050
22126	-4.106679
21185	-3.815206
25784	-3.590991
27002	-3.150986
27023	-3.017249
20502	-2.973199

Genera Escherichia and Shigella Y1

Figure 34: Distribution of the relative abundance of genera Escherichia and Shigella Y1 (n=356)

Outliers values of genera Escherichia and Shigella variable

ident	ch_feces_rel_g4_Y1
25416	13.58948
15960	13.58987
18509	13.60713
27309	13.64755
28119	15.39361
16766	17.23670
22992	17.36016
23769	17.96535
20151	17.97046
21048	18.25990
15066	18.55379
22167	20.25002
19261	20.41874
23076	20.44003
15567	21.39657
25433	21.92901
26806	22.15355
27658	22.91080
23816	23.85316
27706	24.08937
15422	24.20503
21785	25.49000
15741	25.50147
25784	26.09135
27747	27.68118
18501	28.26770
28226	29.34613
21839	33.41706
17664	35.40139
25668	35.83815
22640	36.12863
23271	37.62083
17700	39.83740
27490	41.40386
14173	41.80775
22364	43.11800
23275	45.21610
21511	47.08227
27305	49.40641
20386	50.88671
25943	52.23419
27002	57.71162
26750	58.92070
27954	61.96936
27023	62.53976
15768	64.28868
20502	66.38433
26237	67.04383
28130	74.45240
23330	93.25777

Figure 35: Distribution of the relative abundance of ln(genera Escherichia and Shigella) Y1 (n=356)

Outliers values of genera Escherichia and Shigella variable (ln)

ident	ch_feces_rel_g4_Y1_ln
17095	-Inf
18673	-Inf
20640	-Inf
21967	-Inf
23327	-Inf
25166	-Inf
25913	-Inf
26457	-Inf
27344	-Inf

Covariates

Overview of the potential covariates

484 correspond a la taille d’échantillon total de SEPAGES.

356 correspond à la taille d’échantillon selon les données de microbiote disponibles.

Les effectifs finaux après prise en conmpte des données de neurodeveloppement varient selon la variable de neurodeveloppement et sont visibles dans le flowchart Part 3.

Table 5:

Overview of the potential covariates (distribution and missing data)

Characteristic	Distribution	Missing data	Distribution	Missing data
	N = 4841	N = 4842	N = 3561	N = 3562
Child age at the CBCL 2 years evaluation	106.14 (105.14, 108.00)	67/484 (14%)	106.14 (105.14, 108.14)	20/356 (5.6%)
Child age at the IQ 3 years evaluation	160.3 (158.6, 163.1)	102/484 (21%)	160.3 (158.6, 163.1)	41/356 (12%)
Child age at the SRS 3 years evaluation	158.4 (156.1, 160.9)	65/484 (13%)	158.1 (155.9, 160.4)	15/356 (4.2%)
Birth weight (Kg)	3.28 (3.04, 3.56)	5/484 (1.0%)	3.28 (3.03, 3.58)	0/356 (0%)
Birth weight
<3 Kg	99 (21%)	5/484 (1.0%)	74 (21%)	0/356 (0%)
3-3.4 Kg	236 (49%)	5/484 (1.0%)	174 (49%)	0/356 (0%)
≥3.5 Kg	144 (30%)	5/484 (1.0%)	108 (30%)	0/356 (0%)
Birth length (cm)	50.00 (49.00, 51.50)	12/484 (2.5%)	50.00 (49.00, 51.50)	1/356 (0.3%)
Birth length
<50 cm	170 (36%)	12/484 (2.5%)	130 (37%)	1/356 (0.3%)
50-51 cm	195 (41%)	12/484 (2.5%)	141 (40%)	1/356 (0.3%)
≥52 cm	107 (23%)	12/484 (2.5%)	84 (24%)	1/356 (0.3%)
Weight at one year (Kg)	9.31 (8.71, 10.13)	68/484 (14%)	9.25 (8.71, 10.17)	5/356 (1.4%)
Weight at one year
<8.5 Kg	72 (17%)	68/484 (14%)	61 (17%)	5/356 (1.4%)
8.5-9.9 Kg	228 (55%)	68/484 (14%)	192 (55%)	5/356 (1.4%)
≥10 Kg	116 (28%)	68/484 (14%)	98 (28%)	5/356 (1.4%)
Length at one year (cm)	76.00 (74.00, 78.00)	80/484 (17%)	76.00 (74.00, 78.00)	13/356 (3.7%)
Length at one year
<75 cm	144 (36%)	80/484 (17%)	125 (36%)	13/356 (3.7%)
75-77.9 cm	150 (37%)	80/484 (17%)	124 (36%)	13/356 (3.7%)
≥78 cm	110 (27%)	80/484 (17%)	94 (27%)	13/356 (3.7%)
Weight at 3 years (Kg)	14.45 (13.50, 15.55)	101/484 (21%)	14.38 (13.50, 15.55)	40/356 (11%)
Weight at 3 years
9-13 Kg	126 (33%)	101/484 (21%)	105 (33%)	40/356 (11%)
14 Kg	129 (34%)	101/484 (21%)	107 (34%)	40/356 (11%)
15-20 Kg	128 (33%)	101/484 (21%)	104 (33%)	40/356 (11%)
Length at 3 years (cm)	95.0 (93.0, 97.3)	103/484 (21%)	95.3 (93.0, 97.4)	42/356 (12%)
Length at 3 years
81-93 cm	123 (32%)	103/484 (21%)	96 (31%)	42/356 (12%)
94-95 cm	129 (34%)	103/484 (21%)	110 (35%)	42/356 (12%)
96-106 cm	129 (34%)	103/484 (21%)	108 (34%)	42/356 (12%)
Child sex
Male	256 (53%)	5/484 (1.0%)	190 (53%)	0/356 (0%)
Female	223 (47%)	5/484 (1.0%)	166 (47%)	0/356 (0%)
Maternal education
≥5 years after graduation	272 (56%)	2/484 (0.4%)	201 (57%)	2/356 (0.6%)
3-4 years after graduation	127 (26%)	2/484 (0.4%)	97 (27%)	2/356 (0.6%)
2 years or less after graduation	83 (17%)	2/484 (0.4%)	56 (16%)	2/356 (0.6%)
Maternal education
≥5 years after graduation	272 (56%)	2/484 (0.4%)	201 (57%)	2/356 (0.6%)
<5 years after graduation	210 (44%)	2/484 (0.4%)	153 (43%)	2/356 (0.6%)
Maternal age at conception (years)	32.1 (29.9, 35.2)	0/484 (0%)	32.3 (29.9, 35.2)	0/356 (0%)
Maternal age at conception
20-30 years	161 (33%)	0/484 (0%)	115 (32%)	0/356 (0%)
31-33 years	161 (33%)	0/484 (0%)	119 (33%)	0/356 (0%)
34-44 years	162 (33%)	0/484 (0%)	122 (34%)	0/356 (0%)
Woman living in couple during pregnancy	479 (99%)	0/484 (0%)	353 (99%)	0/356 (0%)
Maternal BMI before pregnancy (kg/m2)	21.5 (19.8, 23.9)	4/484 (0.8%)	21.5 (19.7, 23.7)	1/356 (0.3%)
Maternal BMI before pregnancy
<19 Kg/m2	60 (13%)	4/484 (0.8%)	48 (14%)	1/356 (0.3%)
19-23.9 Kg/m2	301 (63%)	4/484 (0.8%)	223 (63%)	1/356 (0.3%)
≥24 Kg/m2	119 (25%)	4/484 (0.8%)	84 (24%)	1/356 (0.3%)
Maternal parity
0	222 (46%)	0/484 (0%)	164 (46%)	0/356 (0%)
1	214 (44%)	0/484 (0%)	156 (44%)	0/356 (0%)
2	48 (9.9%)	0/484 (0%)	36 (10%)	0/356 (0%)
Maternal parity
None	222 (46%)	0/484 (0%)	164 (46%)	0/356 (0%)
1 child or more	262 (54%)	0/484 (0%)	192 (54%)	0/356 (0%)
Breastfeeding duration (weeks)	26 (13, 43)	43/484 (8.9%)	26 (16, 43)	9/356 (2.5%)
Breastfeeding duration
Not breastfed	40 (9.1%)	43/484 (8.9%)	29 (8.4%)	9/356 (2.5%)
<24 weeks	157 (36%)	43/484 (8.9%)	122 (35%)	9/356 (2.5%)
24-47 weeks	149 (34%)	43/484 (8.9%)	117 (34%)	9/356 (2.5%)
Still breastfeed at 48 weeks	95 (22%)	43/484 (8.9%)	79 (23%)	9/356 (2.5%)
Gestational duration, completed weeks	40.00 (39.00, 40.00)	4/484 (0.8%)	40.00 (39.00, 40.00)	0/356 (0%)
Delivery mode
Vaginal delivery	398 (83%)	5/484 (1.0%)	298 (84%)	0/356 (0%)
C-section	81 (17%)	5/484 (1.0%)	58 (16%)	0/356 (0%)
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	293 (77%)	105/484 (22%)	253 (79%)	37/356 (10%)
Between 6 and 12 months old	66 (17%)	105/484 (22%)	50 (16%)	37/356 (10%)
Not introduced at 12 months old	20 (5.3%)	105/484 (22%)	16 (5.0%)	37/356 (10%)
Presence of pets
No	271 (70%)	98/484 (20%)	222 (71%)	45/356 (13%)
One or more	115 (30%)	98/484 (20%)	89 (29%)	45/356 (13%)
Antibiotics use between 0-12 months old
No	332 (72%)	23/484 (4.8%)	246 (69%)	1/356 (0.3%)
Yes	129 (28%)	23/484 (4.8%)	109 (31%)	1/356 (0.3%)
Learning materials score at 3 years of age (HOME questionnaire)	8.00 (7.00, 9.00)	107/484 (22%)	8.00 (7.00, 9.00)	43/356 (12%)
Language stimulation score at 3 years of age (HOME questionnaire)	6.00 (5.00, 7.00)	107/484 (22%)	6.00 (6.00, 7.00)	43/356 (12%)
Academic stimulation score at 3 years of age (HOME questionnaire)	3.00 (3.00, 4.00)	107/484 (22%)	3.00 (3.00, 4.00)	43/356 (12%)
Variety score at 3 years of age (HOME questionnaire)	7.00 (7.00, 8.00)	107/484 (22%)	7.00 (7.00, 8.00)	43/356 (12%)
HOME questionnaire total score	25.00 (23.00, 26.00)	107/484 (22%)	25.00 (23.00, 26.00)	43/356 (12%)
Maternal anxiety score during the third trimester of pregnancy	6.0 (4.0, 8.0)	44/484 (9.1%)	6.00 (4.00, 8.00)	12/356 (3.4%)
Maternal depression score during the third trimester of pregnancy	4.00 (2.00, 5.00)	45/484 (9.3%)	4.00 (2.00, 5.00)	13/356 (3.7%)
Maternal anxiety and depression score during the third trimester of pregnancy	10.0 (7.0, 13.0)	46/484 (9.5%)	10.0 (7.0, 13.0)	14/356 (3.9%)
Maternal anxiety score when child is one year old	7.0 (5.0, 9.0)	167/484 (35%)	7.0 (5.0, 9.0)	81/356 (23%)
Maternal depression score when child is one year old	3.00 (2.00, 6.00)	167/484 (35%)	3.00 (2.00, 6.00)	81/356 (23%)
Maternal anxiety and depression score when child is one year old	10.0 (8.0, 14.0)	167/484 (35%)	11.0 (8.0, 14.0)	81/356 (23%)
Maternal active smoking during pregnancy
No	401 (93%)	54/484 (11%)	310 (94%)	26/356 (7.3%)
Yes	29 (6.7%)	54/484 (11%)	20 (6.1%)	26/356 (7.3%)
Maternal passive smoking during pregnancy
No	352 (80%)	44/484 (9.1%)	277 (82%)	17/356 (4.8%)
Yes	88 (20%)	44/484 (9.1%)	62 (18%)	17/356 (4.8%)
Child passive smoking during the first year of life
No	340 (78%)	50/484 (10%)	277 (78%)	0/356 (0%)
Yes	94 (22%)	50/484 (10%)	79 (22%)	0/356 (0%)
Child perinatal exposure to tabacco up to one year
No	267 (63%)	63/484 (13%)	224 (66%)	16/356 (4.5%)
Yes	154 (37%)	63/484 (13%)	116 (34%)	16/356 (4.5%)
Child perinatal passive smoking up to one year
No	277 (65%)	61/484 (13%)	232 (67%)	12/356 (3.4%)
Yes	146 (35%)	61/484 (13%)	112 (33%)	12/356 (3.4%)
Maternal alcohol consumption during pregnancy
Did not drink	149 (32%)	23/484 (4.8%)	110 (31%)	4/356 (1.1%)
Drank only before finding out she was pregnant	208 (45%)	23/484 (4.8%)	168 (48%)	4/356 (1.1%)
Drank	104 (23%)	23/484 (4.8%)	74 (21%)	4/356 (1.1%)
Maternal alcohol consumption during pregnancy
Did not drink	149 (32%)	23/484 (4.8%)	110 (31%)	4/356 (1.1%)
Drank only before finding out she was pregnant	208 (45%)	23/484 (4.8%)	168 (48%)	4/356 (1.1%)
<1drink/month when she knew she was pregnant	81 (18%)	23/484 (4.8%)	63 (18%)	4/356 (1.1%)
>1drink/month when she knew she was pregnant	23 (5.0%)	23/484 (4.8%)	11 (3.1%)	4/356 (1.1%)
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	253 (63%)	81/484 (17%)	209 (63%)	25/356 (7.0%)
Other	150 (37%)	81/484 (17%)	122 (37%)	25/356 (7.0%)
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	326 (81%)	81/484 (17%)	271 (82%)	25/356 (7.0%)
Other	77 (19%)	81/484 (17%)	60 (18%)	25/356 (7.0%)
Main mode of child care up to 1 year
Collective day care	334 (83%)	81/484 (17%)	278 (84%)	25/356 (7.0%)
Other	69 (17%)	81/484 (17%)	53 (16%)	25/356 (7.0%)
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	81 (20%)	81/484 (17%)	61 (18%)	25/356 (7.0%)
Nursery assistant (out child home)	172 (43%)	81/484 (17%)	148 (45%)	25/356 (7.0%)
Other	150 (37%)	81/484 (17%)	122 (37%)	25/356 (7.0%)
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	132 (33%)	81/484 (17%)	101 (31%)	25/356 (7.0%)
Nursery assistant (out child home)	194 (48%)	81/484 (17%)	170 (51%)	25/356 (7.0%)
Other	77 (19%)	81/484 (17%)	60 (18%)	25/356 (7.0%)
Main mode of child care up to 1 year
Collective day care	135 (33%)	81/484 (17%)	104 (31%)	25/356 (7.0%)
Nursery assistant (out child home)	199 (49%)	81/484 (17%)	174 (53%)	25/356 (7.0%)
Other	69 (17%)	81/484 (17%)	53 (16%)	25/356 (7.0%)
Paternal ethinicity
Caucassian	390 (95%)	74/484 (15%)	304 (95%)	35/356 (9.8%)
Others	20 (4.9%)	74/484 (15%)	17 (5.3%)	35/356 (9.8%)
Paternal education
≥5 years after graduation	189 (64%)	190/484 (39%)	157 (64%)	110/356 (31%)
3-4 years after graduation	49 (17%)	190/484 (39%)	41 (17%)	110/356 (31%)
2 years or less after graduation	56 (19%)	190/484 (39%)	48 (20%)	110/356 (31%)
Paternal age at child birth (years)	34.4 (31.6, 38.0)	82/484 (17%)	34.4 (31.6, 37.9)	39/356 (11%)
Paternal age at child birth
23-31 years	134 (33%)	82/484 (17%)	106 (33%)	39/356 (11%)
32-36 years	134 (33%)	82/484 (17%)	106 (33%)	39/356 (11%)
37-72 years	134 (33%)	82/484 (17%)	105 (33%)	39/356 (11%)
Maternal ethnicity
Caucassian	445 (96%)	21/484 (4.3%)	341 (97%)	3/356 (0.8%)
Others	18 (3.9%)	21/484 (4.3%)	12 (3.4%)	3/356 (0.8%)
Child age at stool collection (weeks)	53.6 (52.2, 55.4)	131/484 (27%)	53.5 (52.2, 55.4)	7/356 (2.0%)
MiSeq analytic batch effect
R2	218 (61%)	128/484 (26%)	218 (61%)	0/356 (0%)
R3	138 (39%)	128/484 (26%)	138 (39%)	0/356 (0%)
1 Median (IQR); n (%)
2 N missing/No. obs. (% missing); N missing/No. obs. (% missing)

Continuous covariates

Table 6: Description of the continuous covariates

Variable labels	Min	Q1	Median	Mean	Q3	Max	N	W_statistic_shapiro	p_value_shapiro
Child age at the CBCL 2 years evaluation	100	105	106	106.7	108	121	417	0.9	<0.001
Child age at the IQ 3 years evaluation	144	159	160	161.3	163	184	382	0.9	<0.001
Child age at the SRS 3 years evaluation	144	156	158	159.0	161	198	419	0.9	<0.001
Birth weight (Kg)	1	3	3	3.3	4	5	479	1	<0.001
Birth length (cm)	36	49	50	50.1	52	59	472	0.9	<0.001
Weight at one year (Kg)	6	9	9	9.4	10	13	416	1	<0.001
Length at one year (cm)	68	74	76	76.0	78	84	404	1	2.069817e-01
Weight at 3 years (Kg)	9	14	14	14.6	16	20	383	1	7.891381e-03
Length at 3 years (cm)	81	93	95	95.2	97	106	381	1	6.023938e-02
Maternal age at conception (years)	21	30	32	32.5	35	45	484	1	6.554413e-02
Maternal BMI before pregnancy (kg/m2)	17	20	22	22.4	24	42	480	0.8	<0.001
Breastfeeding duration (weeks)	0	13	26	26.6	43	48	441	0.9	<0.001
Gestational duration, completed weeks	28	39	40	39.2	40	42	480	0.8	<0.001
Learning materials score at 3 years of age (HOME questionnaire)	4	7	8	8.0	9	11	377	0.9	<0.001
Language stimulation score at 3 years of age (HOME questionnaire)	2	5	6	6.0	7	7	377	0.8	<0.001
Academic stimulation score at 3 years of age (HOME questionnaire)	0	3	3	3.3	4	5	377	0.9	<0.001
Variety score at 3 years of age (HOME questionnaire)	4	7	7	7.3	8	11	377	0.9	<0.001
HOME questionnaire total score	16	23	25	24.5	26	32	377	1	<0.001
Maternal anxiety score during the third trimester of pregnancy	0	4	6	6.4	8	18	440	1	<0.001
Maternal depression score during the third trimester of pregnancy	0	2	4	4.2	5	19	439	0.9	<0.001
Maternal anxiety and depression score during the third trimester of pregnancy	2	7	10	10.6	13	37	438	0.9	<0.001
Maternal anxiety score when child is one year old	1	5	7	7.2	9	17	317	1	<0.001
Maternal depression score when child is one year old	0	2	3	3.9	6	14	317	0.9	<0.001
Maternal anxiety and depression score when child is one year old	2	8	10	11.1	14	31	317	1	<0.001
Paternal age at child birth (years)	24	32	34	35.2	38	73	402	0.9	<0.001
Child age at stool collection (weeks)	48	52	54	54.2	55	70	353	0.9	<0.001

Figure 36: Spearman correlations between continuous covariates

Child age at the CBCL 2 years evaluation

Figure 37: Distribution of child age at the CBCL 2 years evaluation (n = 417/484)

Outliers values of child age at CBCL 2 years test variable

ident	ch_age_CBCL_Y2
24246	99.85714
14638	112.42857
18673	112.57143
18501	112.71429
20306	113.00000
25784	113.00000
21511	113.14286
26457	113.28571
21112	113.85714
14461	114.00000
23994	114.00000
19954	115.14286
25409	115.42857
24298	116.00000
27015	116.71429
23250	117.85714
23258	120.71429

Child age at the IQ 3 years evaluation

Figure 38: Distribution of child age at the IQ 3 years evaluation (n = 382/484)

Outliers values of child age at IQ 3 years test variable

ident	ch_age_IQ_Y3
17465	143.5714
16650	170.0000
25344	170.1429
25572	170.7143
25773	170.8571
14177	171.2857
26136	171.5714
14184	171.7143
27943	171.7143
27866	172.4286
22620	173.0000
15960	173.4286
14013	173.7143
25784	175.0000
26882	180.2857
17115	183.7143

Child age at the SRS and BRIEF-P 3 years evaluation

Figure 39: Distribution of child age at the SRS and BRIEF-P 3 years evaluation (n = 419/484)

Outliers values of child age at SRS and BRIEF-P 3 years variable

ident	ch_age_SRS_BRIEFP_Y3
17465	143.5714
27084	168.2857
28021	168.7143
26806	169.4286
15704	169.8571
17906	169.8571
22672	170.4286
23696	171.4286
27943	172.2857
22620	173.0000
14013	173.7143
23994	176.0000
21271	176.4286
14638	178.4286
26882	197.5714

Paternal age at child birth (years)

Figure 40: Distribution of paternal age at child birth (years) (n = 402/484)

Outliers values of paternal age at child birth variable

ident	fa_age
20905	48.84110
26539	49.09863
26882	50.93425
18086	55.10137
14886	57.95068
22620	72.57808

Maternal age at conception (years)

Figure 41: Distribution of maternal age at conception (years) (n = 484/484)

Outliers values of maternal age during pregnancy variable

ident	mo_age
15370	20.56400
15929	44.87337
22620	45.32512
20905	45.47023

Maternal BMI before pregnancy (kg/m2)

Figure 42: Distribution of maternal BMI before pregnancy (kg/m2) (n = 480/484)

Outliers values of maternal BMI before pregnancy variable

ident	mo_bmi_bepr
25668	30.33111
15066	30.39341
18700	30.48316
16088	30.58181
27871	31.08530
18673	31.13306
16093	31.67393
14934	31.78093
26871	31.93935
19216	33.05785
17585	34.18245
23475	35.11111
24897	35.93750
23327	36.71875
25806	38.66746
16782	40.25726
22042	41.27022
18721	41.83683
27442	41.95202

Maternal anxiety score during the third trimester of pregnancy

Figure 43: Distribution of maternal anxiety score during the third trimester of pregnancy (n = 440/484)

Outliers values of maternal anxiety score T3 variable

ident	mo_hadanxscore_grt3_imp
14433	15
14732	15
15034	15
18873	15
25166	15
17717	16
16294	17
19125	17
16088	18

Maternal depression score during the third trimester of pregnancy

Figure 44: Distribution of maternal depression score during the third trimester of pregnancy (years) (n = 439/484)

Outliers values of maternal depression score T3 variable

ident	mo_haddepscore_grt3_imp
14184	10
14680	10
15326	10
15713	10
16786	10
18721	10
19971	10
20536	10
20905	10
23020	10
23250	10
25409	10
25668	10
27539	10
14276	11
14930	11
18199	11
23475	11
23974	11
17248	12
22042	12
14433	13
23076	13
23306	14
27305	14
16294	18
16088	19

Maternal anxiety and depression score during the third trimester of pregnancy

Figure 45: Distribution of maternal anxiety and depression score during the third trimester of pregnancy (n = 438/484)

Outliers values of maternal anxiety and depression score T3 variable

ident	mo_hadtotscore_grt3_imp
15034	23
18873	23
19125	23
20536	23
23306	23
14732	24
23076	25
23475	25
14433	28
16294	35
16088	37

Maternal anxiety score when child is one year old

Figure 46: Distribution of maternal anxiety score when child is one year old (n = 317/484)

Outliers values of maternal anxiety score at 1 year variable

ident	mo_hadanxscore_y1_imp
15645	16
17906	16
17764	17
19764	17
23603	17

Maternal depression score when child is one year old

Figure 47: Distribution of maternal depression score when child is one year old(n = 317/484)

Outliers values of maternal depression score at 1 year variable

ident	mo_haddepscore_y1_imp
27316	13
14732	14
17764	14
28047	14

Maternal anxiety and depression score when child is one year old

Figure 48: Distribution of maternal anxiety and depression score when child is one year old (n = 317/484)

Outliers values of maternal anxiety and depression score at 1 year variable

ident	mo_hadtotscore_y1_imp
24359	24
14732	25
23603	25
28119	25
17906	26
17764	31

Breastfeeding duration (weeks)

Figure 49: Distribution of breastfeeding duration (weeks) (n = 441/484)

Breastfeeding duration variable doesn’t have outliers.

Gestational duration (completed weeks)

Figure 50: Distribution of gestational duration (completed weeks) (n = 480/484)

Outliers values of gestational age variable

ident	po_gd
14886	28
17827	30
15929	32
16815	33
25668	33
25943	33
14880	34
23901	35
26136	35
26760	35
27666	35
14548	36
15075	36
15821	36
15921	36
18186	36
18780	36
20536	36
22620	36
23076	36
23306	36
24829	36
25565	36
26891	36
14412	37
14433	37
14461	37
15239	37
15836	37
16021	37
16490	37
16546	37
17248	37
18553	37
18700	37
19125	37
19339	37
20110	37
21271	37
21519	37
22772	37
22812	37
23610	37
23957	37
25337	37
25509	37
25806	37
26168	37
26237	37
27442	37
27650	37
28130	37
27490	42

Child age at stool collection (weeks)

Figure 51: Distribution of child age at stool collection (weeks) (n = 353/484)

Outliers values of child at at stool collection variable

ident	ch_feces_age_w_Y1
28021	60.19048
27201	60.40476
27442	60.79563
16407	60.79762
27526	61.07887
20640	61.36756
24587	61.62202
15186	62.08482
26136	62.19345
27943	62.22272
14638	62.91518
21271	62.93651
14680	63.65575
14567	64.52827
17958	65.24058
22118	65.48760
27866	65.66925
27871	67.57143
15487	68.40377
26882	69.83284
21148	70.37063

Learning materials score at 3 years of age (HOME questionnaire)

Figure 52: Distribution of learning materials score at 3 years of age (n = 377/484)

Learning materials score at 3 years of age (HOME questionnaire) variable doesn’t have outliers.

Language stimulation score at 3 years of age (HOME questionnaire)

Figure 53: Distribution of language stimulation score at 3 years of age (n = 377/484)

Language stimulation score at 3 years of age (HOME questionnaire) variable doesn’t have outliers.

Academic stimulation score at 3 years of age (HOME questionnaire)

Figure 54: Distribution of academic stimulation score at 3 years of age (n = 377/484)

Outliers values of home_academic_y3 variable

ident	home_academic_y3
14567	0
14895	0
15171	0
18868	0
14576	1
14856	1
14958	1
15186	1
15218	1
16782	1
17138	1
23306	1
24335	1
28066	1

Variety score at 3 years of age (HOME questionnaire)

Figure 55: Distribution of variety score at 3 years of age (n = 377/484)

Outliers values of home_variety_y3 variable

ident	home_variety_y3
15813	4
16546	4
27658	4
14930	5
15034	5
15186	5
15218	5
15367	5
16435	5
16766	5
17095	5
17668	5
17708	5
18581	5
19677	5
22198	5
22388	5
25043	5
25409	5
25509	5
26237	5
27567	5
27747	5
27915	5
14557	11

HOME questionnaire total score

Figure 56: Distribution of HOME questionnaire total score (n = 377/484)

Outliers values of home_total_y3 variable

ident	home_total_y3
15171	16
15186	17
18868	17
15218	18
15813	18
16546	18
22957	31
25337	31
26760	31
19387	32

Birth weight (Kg)

Figure 57: Distribution of birth weight (Kg) (n = 479/484)

Outliers values of child weight at birth variable

ident	po_w_kg
17827	0.995
14886	1.015
15929	1.880
23076	1.880
19587	2.070
14412	2.160
24829	2.170
26760	2.190
25565	2.200
24485	4.480
19418	4.520
27058	4.590
23371	4.670

Birth length (cm)

Figure 58: Distribution of birth length (cm) (n = 472/484)

Outliers values of child length at birth variable

ident	po_he
17827	36.4
14886	38.0
15929	42.5
23076	42.5
26760	43.0
14880	44.0
24829	44.0
14412	45.0
16179	45.0
16815	45.0
16958	55.5
19261	56.0
19708	56.0
14476	57.0
17708	57.5
23924	58.5

Weight at one year (Kg)

Figure 59: Distribution of weight at one year (Kg) (n = 416/484)

Outliers values of child weight at one year variable

ident	ch_w_Y1
24829	6.0175
22388	12.8850
18721	13.3850

Length at one year (cm)

Figure 60: Distribution of length at one year (cm) (n = 404/484)

Outliers values of child length at one year variable

ident	ch_he_Y1
24829	67.75

Weight at 3 years (Kg)

Figure 61: Distribution of weight at 3 years (Kg) (n = 383/484)

Outliers values of child weight at 3 years variable

ident	ch_w_Y3
24829	9.15
16088	18.65
22223	18.65
22388	18.75
20098	19.30
22288	19.35
17617	19.50

Length at 3 years (cm)

Les enfants avec les ident “27309”, “17668” et “17958” ont été passé en données manquantes car les valeurs taille à 3 ans étaient improbables (environ égales à 10 cm)

Figure 62: Distribution of length at 3 years (cm) (n = 381/484)

Outliers values of child length at 3 years variable

ident	ch_he_Y3
24829	81.00
25913	86.00
16179	86.25
26117	86.25
20194	86.50
22388	104.00
24127	104.00
25915	104.25
22288	105.00
20151	105.50
28021	106.00

Part 2: Choice of covariates and their coding

Directed acyclic graph

Figure 63: Directed acyclic graph

Ici on teste :

• toutes les covariables potentielles identifiées avec le DAG (Univariates models)
• 1 modèle multivarié en modèle univarié toutes les covariables potentielles (Multivariate model test 1, avant inclusion des variables d’intérêt) :
  • les covariables de ce modèles sont :
    • var_age (âge de l’enfant lors du test de neurodeveloppement)
    • po_w_kg_3cat (poids de l’enfant à la naissance
    • po_he_3cat (taille de l’enfant à la naissance
    • mo_dipl_2cat (niveau de diplome de la mère)
    • mo_age (âge maternel)
    • mo_bmi_bepr_3cat (IMC maternel avant la grossesse)
    • ch_sex (sexe de l’enfant)
    • mo_par_2cat (parité)
    • ch_bf_duration_till48w_4cat (durée de la l’allaitement)
    • po_gd (durée de la gestation)
    • po_delmod (mode d’accouchement
    • ch_food_intro_Y1_3cat (période d’introduction de la nourriture solide)
    • mo_pets (présence d’animaux)
    • ch_antibio_Y1_2cat (prise d’antibiotique entre la naissance et l’âge de 1 an)
    • home_total_y3 (score HOME à 3 ans)
    • mo_hadtotscore_grt3_imp (score d’anxiété et de dépression de la mère lors du 3ème trimestre de la grossesse)
    • mo_tob_gr_anyt_yn_n2 (tabagisme actif de la mère pendant la grossesse)
    • ch_tabacco_passive_up_to_Y1 (tabagisme périnatal passif de l’enfant (tabagisme passif de la mère pendant la grossesse + tabagisme passif de l’enfant de la naissance à l’âge de 1 an)
    • ch_care_main_12m_opt2_2c (mode de garde principal de l’enfant à l’âge de 1 an)
  • La différence avec le deuxième modèle multivarié porte sur la variable mode de garde
• 1 modèle multivarié en modèle univarié toutes les covariables potentielles (Multivariate model test 1, avant inclusion des variables d’intérêt) :
  • les covariables de ce modèles sont :
    • var_age (âge de l’enfant lors du test de neurodeveloppement)
    • po_w_kg_3cat (poids de l’enfant à la naissance
    • po_he_3cat (taille de l’enfant à la naissance
    • mo_dipl_2cat (niveau de diplome de la mère)
    • mo_age (âge maternel)
    • mo_bmi_bepr_3cat (IMC maternel avant la grossesse)
    • ch_sex (sexe de l’enfant)
    • mo_par_2cat (parité)
    • ch_bf_duration_till48w_4cat (durée de la l’allaitement)
    • po_gd (durée de la gestation)
    • po_delmod (mode d’accouchement
    • ch_food_intro_Y1_3cat (période d’introduction de la nourriture solide)
    • mo_pets (présence d’animaux)
    • ch_antibio_Y1_2cat (prise d’antibiotique entre la naissance et l’âge de 1 an)
    • home_total_y3 (score HOME à 3 ans)
    • mo_hadtotscore_grt3_imp (score d’anxiété et de dépression de la mère lors du 3ème trimestre de la grossesse)
    • mo_tob_gr_anyt_yn_n2 (tabagisme actif de la mère pendant la grossesse)
    • ch_tabacco_passive_up_to_Y1 (tabagisme périnatal passif de l’enfant (tabagisme passif de la mère pendant la grossesse + tabagisme passif de l’enfant de la naissance à l’âge de 1 an)
    • ch_care_main_6m_12m_opt2_2c (mode de garde principal de l’enfant jusqu’à l’âge de 1 an)
  • La différence avec le premier modèle multivarié porte sur la variable mode de garde

Tous les outcomes sont en continue, sans transformation.

Les variables de microbiote ne sont pas encore inclues dans ces modèles.

CBCL 2Y

Interne score Y2

Table 7:

Influence of maternal and child characteristics on the CBCL interne score at 2 years.

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3361	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	336	0.5	-0.6, 1.6	0.367
Birth weight
<3 Kg	70 (21%)	—	—		—	—		—	—
3-3.4 Kg	166 (49%)	0.8	-0.6, 2.1	0.265	1.0	-0.6, 2.6	0.215	0.9	-0.6, 2.5	0.240
≥3.5 Kg	100 (30%)	0.9	-0.6, 2.3	0.246	1.5	-0.5, 3.5	0.149	1.4	-0.6, 3.4	0.161
Birth length (cm)	335	0.0	-0.2, 0.3	0.749
Birth length
<50 cm	123 (37%)	—	—		—	—		—	—
50-51 cm	135 (40%)	0.2	-1.0, 1.3	0.783	-0.3	-1.7, 1.1	0.701	-0.3	-1.7, 1.1	0.706
≥52 cm	77 (23%)	0.0	-1.4, 1.4	0.995	-0.6	-2.4, 1.3	0.560	-0.5	-2.4, 1.3	0.576
Weight at one year (Kg)	331	-0.1	-0.6, 0.4	0.648
Weight at one year
<8.5 Kg	61 (18%)	—	—
8.5-9.9 Kg	181 (55%)	-0.4	-1.8, 1.0	0.593
≥10 Kg	89 (27%)	-0.4	-2.0, 1.2	0.630
Length at one year (cm)	324	-0.1	-0.3, 0.1	0.263
Length at one year
<75 cm	121 (37%)	—	—
75-77.9 cm	118 (36%)	-1.5	-2.7, -0.3	0.012
≥78 cm	85 (26%)	-0.7	-2.0, 0.5	0.259
Weight at 3 years (Kg)	307	-0.2	-0.6, 0.1	0.142
Weight at 3 years
9-13 Kg	104 (34%)	—	—
14 Kg	103 (34%)	-1.3	-2.6, 0.0	0.052
15-20 Kg	100 (33%)	-0.8	-2.1, 0.5	0.227
Length at 3 years (cm)	306	-0.1	-0.3, 0.0	0.125
Length at 3 years
81-93 cm	94 (31%)	—	—
94-95 cm	109 (36%)	-0.2	-1.5, 1.2	0.802
96-106 cm	103 (34%)	-0.7	-2.0, 0.7	0.327
Child sex
Male	181 (54%)	—	—		—	—		—	—
Female	155 (46%)	0.2	-0.9, 1.2	0.739	0.6	-0.5, 1.7	0.295	0.6	-0.5, 1.7	0.308
Maternal education
≥5 years after graduation	191 (57%)	—	—
3-4 years after graduation	91 (27%)	0.0	-1.2, 1.2	0.977
2 years or less after graduation	52 (16%)	0.4	-1.1, 1.9	0.611
Maternal education
≥5 years after graduation	191 (57%)	—	—		—	—		—	—
<5 years after graduation	143 (43%)	0.1	-0.9, 1.2	0.777	-0.2	-1.2, 0.9	0.762	-0.2	-1.2, 0.9	0.747
Maternal age at conception (years)	336	-0.1	-0.3, 0.0	0.049	-0.1	-0.3, 0.0	0.147	-0.1	-0.3, 0.0	0.142
Maternal BMI before pregnancy (kg/m2)	335	0.0	-0.1, 0.2	0.563
Maternal BMI before pregnancy
<19 Kg/m2	47 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	209 (62%)	0.1	-1.4, 1.7	0.856	0.4	-1.1, 1.9	0.622	0.4	-1.1, 1.9	0.600
≥24 Kg/m2	79 (24%)	0.6	-1.1, 2.3	0.489	0.5	-1.2, 2.3	0.572	0.5	-1.3, 2.2	0.581
Maternal parity
None	157 (47%)	—	—		—	—		—	—
1 child or more	179 (53%)	-1.2	-2.2, -0.2	0.022	-1.5	-2.7, -0.4	0.009	-1.6	-2.7, -0.4	0.008
Breastfeeding duration
Not breastfed	28 (8.5%)	—	—		—	—		—	—
<24 weeks	114 (35%)	-0.2	-2.2, 1.8	0.833	-0.1	-2.1, 1.9	0.952	0.0	-2.0, 2.0	0.962
24-47 weeks	113 (34%)	-0.3	-2.3, 1.7	0.803	0.1	-1.9, 2.2	0.887	0.2	-1.9, 2.2	0.876
Still breastfeed at 48 weeks	73 (22%)	0.8	-1.3, 2.9	0.434	0.9	-1.1, 3.0	0.375	0.9	-1.2, 3.0	0.392
Gestational duration, completed weeks	336	0.2	-0.1, 0.5	0.229	0.1	-0.3, 0.5	0.648	0.1	-0.3, 0.5	0.619
Delivery mode
Vaginal delivery	282 (84%)	—	—		—	—		—	—
C-section	54 (16%)	-0.2	-1.6, 1.2	0.805	-0.4	-1.9, 1.1	0.595	-0.4	-1.8, 1.1	0.631
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	247 (80%)	—	—		—	—		—	—
Between 6 and 12 months old	47 (15%)	-0.1	-1.6, 1.5	0.946	-0.7	-2.3, 0.9	0.365	-0.8	-2.4, 0.9	0.352
Not introduced at 12 months old	13 (4.2%)	-0.7	-3.4, 2.0	0.588	0.5	-2.4, 3.3	0.746	0.4	-2.4, 3.2	0.761
Presence of pets
No	214 (72%)	—	—		—	—		—	—
One or more	83 (28%)	0.3	-0.9, 1.5	0.589	0.3	-1.0, 1.6	0.648	0.3	-1.0, 1.6	0.666
Antibiotics use between 0-12 months old
No	230 (69%)	—	—		—	—		—	—
Yes	105 (31%)	-0.7	-1.8, 0.4	0.220	-0.6	-1.8, 0.5	0.279	-0.6	-1.8, 0.5	0.277
Learning materials score at 3 years of age (HOME questionnaire)	302	-0.3	-0.7, 0.1	0.124
Language stimulation score at 3 years of age (HOME questionnaire)	302	-0.6	-1.3, 0.1	0.094
Academic stimulation score at 3 years of age (HOME questionnaire)	302	0.0	-0.6, 0.6	0.938
Variety score at 3 years of age (HOME questionnaire)	302	-0.4	-0.9, 0.1	0.091
HOME questionnaire total score	302	-0.2	-0.4, 0.0	0.050	-0.2	-0.4, 0.0	0.096	-0.2	-0.4, 0.0	0.093
Maternal anxiety score during the third trimester of pregnancy	329	0.3	0.1, 0.5	0.001
Maternal depression score during the third trimester of pregnancy	327	0.3	0.1, 0.4	0.008
Maternal anxiety and depression score during the third trimester of pregnancy	327	0.2	0.1, 0.3	<0.001	0.2	0.1, 0.4	<0.001	0.2	0.1, 0.4	<0.001
Maternal anxiety score when child is one year old	268	0.4	0.3, 0.6	<0.001
Maternal depression score when child is one year old	268	0.5	0.3, 0.7	<0.001
Maternal anxiety and depression score when child is one year old	268	0.3	0.2, 0.5	<0.001
Maternal active smoking during pregnancy
No	294 (94%)	—	—		—	—		—	—
Yes	18 (5.8%)	-0.1	-2.3, 2.1	0.926	-0.2	-2.8, 2.4	0.888	-0.2	-2.8, 2.4	0.892
Maternal passive smoking during pregnancy
No	262 (81%)	—	—
Yes	61 (19%)	1.3	0.0, 2.7	0.051
Child passive smoking during the first year of life
No	259 (77%)	—	—
Yes	77 (23%)	1.1	-0.1, 2.3	0.081
Child perinatal exposure to tabacco up to one year
No	210 (65%)	—	—
Yes	112 (35%)	1.1	0.0, 2.2	0.052
Child perinatal passive smoking up to one year
No	217 (67%)	—	—		—	—		—	—
Yes	109 (33%)	1.2	0.1, 2.3	0.040	0.9	-0.3, 2.0	0.127	0.9	-0.3, 2.0	0.125
Maternal alcohol consumption during pregnancy
Did not drink	105 (32%)	—	—
Drank only before finding out she was pregnant	158 (47%)	-2.1	-3.3, -1.0	<0.001
Drank	70 (21%)	-1.9	-3.3, -0.5	0.009
Maternal alcohol consumption during pregnancy
Did not drink	105 (32%)	—	—
Drank only before finding out she was pregnant	158 (47%)	-2.1	-3.3, -1.0	<0.001
<1drink/month when she knew she was pregnant	59 (18%)	-1.9	-3.4, -0.4	0.012
>1drink/month when she knew she was pregnant	11 (3.3%)	-1.8	-4.8, 1.1	0.215
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	199 (63%)	—	—
Other	118 (37%)	-0.3	-1.4, 0.8	0.571
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	260 (82%)	—	—		—	—
Other	57 (18%)	-0.4	-1.8, 0.9	0.531	-0.5	-2.0, 0.9	0.473
Main mode of child care up to 1 year
Collective day care	266 (84%)	—	—					—	—
Other	51 (16%)	-0.1	-1.5, 1.4	0.912				-0.1	-1.6, 1.4	0.864
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	59 (19%)	—	—
Nursery assistant (out child home)	140 (44%)	0.2	-1.3, 1.7	0.794
Other	118 (37%)	-0.2	-1.7, 1.3	0.816
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	98 (31%)	—	—
Nursery assistant (out child home)	162 (51%)	0.1	-1.1, 1.3	0.824
Other	57 (18%)	-0.4	-1.9, 1.2	0.658
Main mode of child care up to 1 year
Collective day care	101 (32%)	—	—
Nursery assistant (out child home)	165 (52%)	-0.1	-1.3, 1.1	0.883
Other	51 (16%)	-0.1	-1.8, 1.5	0.868
Paternal education
≥5 years after graduation	152 (64%)	—	—
3-4 years after graduation	40 (17%)	1.2	-0.5, 2.9	0.164
2 years or less after graduation	46 (19%)	-0.2	-1.8, 1.4	0.849
Paternal age at child birth (years)	301	-0.2	-0.3, -0.1	<0.001
Paternal age at child birth
23-31 years	97 (32%)	—	—
32-36 years	105 (35%)	-1.1	-2.4, 0.2	0.092
37-72 years	99 (33%)	-2.2	-3.6, -0.9	<0.001
Child age at the CBCL 2 years evaluation	336	0.1	-0.1, 0.3	0.292
Child age at the CBCL 2 years evaluation					0.1	-0.1, 0.3	0.365	0.1	-0.1, 0.3	0.380
No. Obs.					336			336
R²					0.125			0.123
Adjusted R²					0.054			0.052
1 N; n (%)
2 CI = Confidence Interval

Figure 64: Multivariate model hypothesis checking (outcome is CBCL interne score Y2, before inclusion of microbiota variables)

Externe score Y2

Table 8:

Influence of maternal and child characteristics on the CBCL externe score at 2 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3351	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	335	0.2	-1.3, 1.7	0.786
Birth weight
<3 Kg	70 (21%)	—	—		—	—		—	—
3-3.4 Kg	166 (50%)	0.0	-1.7, 1.8	0.981	-0.5	-2.7, 1.6	0.611	-0.6	-2.7, 1.5	0.571
≥3.5 Kg	99 (30%)	0.5	-1.5, 2.4	0.630	-0.1	-2.8, 2.6	0.940	-0.1	-2.8, 2.5	0.914
Birth length (cm)	334	0.0	-0.3, 0.3	0.913
Birth length
<50 cm	123 (37%)	—	—		—	—		—	—
50-51 cm	134 (40%)	0.2	-1.3, 1.7	0.801	-0.3	-2.1, 1.6	0.789	-0.2	-2.1, 1.6	0.795
≥52 cm	77 (23%)	0.6	-1.2, 2.4	0.545	0.1	-2.4, 2.6	0.917	0.2	-2.4, 2.7	0.900
Weight at one year (Kg)	330	0.0	-0.6, 0.7	0.888
Weight at one year
<8.5 Kg	61 (18%)	—	—
8.5-9.9 Kg	180 (55%)	0.7	-1.2, 2.5	0.472
≥10 Kg	89 (27%)	0.5	-1.6, 2.5	0.645
Length at one year (cm)	323	-0.1	-0.3, 0.2	0.598
Length at one year
<75 cm	121 (37%)	—	—
75-77.9 cm	117 (36%)	0.1	-1.5, 1.7	0.912
≥78 cm	85 (26%)	0.6	-1.1, 2.3	0.500
Weight at 3 years (Kg)	306	0.0	-0.4, 0.4	0.973
Weight at 3 years
9-13 Kg	104 (34%)	—	—
14 Kg	102 (33%)	-0.5	-2.2, 1.3	0.581
15-20 Kg	100 (33%)	0.2	-1.5, 2.0	0.802
Length at 3 years (cm)	305	0.0	-0.2, 0.2	0.827
Length at 3 years
81-93 cm	94 (31%)	—	—
94-95 cm	108 (35%)	1.6	-0.2, 3.3	0.075
96-106 cm	103 (34%)	0.0	-1.7, 1.8	0.986
Child sex
Male	180 (54%)	—	—		—	—		—	—
Female	155 (46%)	-0.9	-2.2, 0.5	0.217	-0.3	-1.8, 1.2	0.702	-0.3	-1.8, 1.2	0.690
Maternal education
≥5 years after graduation	191 (57%)	—	—
3-4 years after graduation	90 (27%)	1.1	-0.4, 2.7	0.157
2 years or less after graduation	52 (16%)	1.4	-0.5, 3.3	0.159
Maternal education
≥5 years after graduation	191 (57%)	—	—		—	—		—	—
<5 years after graduation	142 (43%)	1.2	-0.1, 2.6	0.078	0.7	-0.7, 2.1	0.304	0.7	-0.7, 2.1	0.313
Maternal age at conception (years)	335	-0.2	-0.3, 0.0	0.065	-0.2	-0.4, 0.0	0.053	-0.2	-0.4, 0.0	0.052
Maternal BMI before pregnancy (kg/m2)	334	0.1	-0.1, 0.3	0.178
Maternal BMI before pregnancy
<19 Kg/m2	47 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	209 (63%)	0.9	-1.1, 2.9	0.387	0.9	-1.1, 3.0	0.383	0.9	-1.1, 3.0	0.372
≥24 Kg/m2	78 (23%)	0.9	-1.4, 3.2	0.432	0.7	-1.6, 3.1	0.547	0.7	-1.6, 3.1	0.554
Maternal parity
None	157 (47%)	—	—		—	—		—	—
1 child or more	178 (53%)	-0.1	-1.4, 1.3	0.930	-0.2	-1.7, 1.3	0.811	-0.2	-1.7, 1.3	0.770
Breastfeeding duration
Not breastfed	28 (8.6%)	—	—		—	—		—	—
<24 weeks	113 (35%)	-0.5	-3.1, 2.2	0.727	-0.1	-2.8, 2.6	0.941	-0.1	-2.8, 2.6	0.947
24-47 weeks	113 (35%)	-0.8	-3.4, 1.8	0.556	0.1	-2.6, 2.8	0.942	0.1	-2.6, 2.8	0.935
Still breastfeed at 48 weeks	73 (22%)	0.0	-2.8, 2.7	0.974	0.4	-2.4, 3.2	0.777	0.4	-2.4, 3.2	0.797
Gestational duration, completed weeks	335	0.1	-0.3, 0.6	0.557	0.1	-0.4, 0.6	0.663	0.1	-0.4, 0.7	0.639
Delivery mode
Vaginal delivery	281 (84%)	—	—		—	—		—	—
C-section	54 (16%)	0.1	-1.8, 1.9	0.939	-0.1	-2.1, 1.9	0.934	0.0	-2.0, 1.9	0.968
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	247 (80%)	—	—		—	—		—	—
Between 6 and 12 months old	47 (15%)	-0.4	-2.4, 1.6	0.701	-0.8	-2.8, 1.3	0.469	-0.8	-2.8, 1.3	0.454
Not introduced at 12 months old	13 (4.2%)	0.6	-2.9, 4.2	0.718	0.8	-3.0, 4.6	0.672	0.8	-3.1, 4.6	0.690
Presence of pets
No	214 (72%)	—	—		—	—		—	—
One or more	83 (28%)	-0.9	-2.5, 0.7	0.273	-1.1	-2.7, 0.5	0.183	-1.1	-2.7, 0.5	0.180
Antibiotics use between 0-12 months old
No	229 (69%)	—	—		—	—		—	—
Yes	105 (31%)	0.3	-1.2, 1.8	0.694	0.4	-1.1, 1.9	0.629	0.4	-1.1, 1.9	0.634
Learning materials score at 3 years of age (HOME questionnaire)	301	-0.5	-1.1, 0.0	0.046
Language stimulation score at 3 years of age (HOME questionnaire)	301	-0.6	-1.5, 0.3	0.212
Academic stimulation score at 3 years of age (HOME questionnaire)	301	-0.5	-1.3, 0.3	0.226
Variety score at 3 years of age (HOME questionnaire)	301	-0.6	-1.3, 0.0	0.058
HOME questionnaire total score	301	-0.4	-0.6, -0.1	0.010	-0.3	-0.6, 0.0	0.044	-0.3	-0.6, 0.0	0.042
Maternal anxiety score during the third trimester of pregnancy	328	0.4	0.1, 0.6	0.003
Maternal depression score during the third trimester of pregnancy	326	0.2	0.0, 0.5	0.098
Maternal anxiety and depression score during the third trimester of pregnancy	326	0.2	0.1, 0.3	0.005	0.2	0.1, 0.4	0.004	0.2	0.1, 0.4	0.004
Maternal anxiety score when child is one year old	268	0.4	0.2, 0.7	0.002
Maternal depression score when child is one year old	268	0.4	0.1, 0.7	0.006
Maternal anxiety and depression score when child is one year old	268	0.3	0.1, 0.5	<0.001
Maternal active smoking during pregnancy
No	294 (94%)	—	—		—	—		—	—
Yes	18 (5.8%)	2.8	-0.3, 5.8	0.072	1.6	-1.4, 4.6	0.282	1.6	-1.3, 4.6	0.280
Maternal passive smoking during pregnancy
No	262 (81%)	—	—
Yes	61 (19%)	1.7	-0.1, 3.4	0.059
Child passive smoking during the first year of life
No	258 (77%)	—	—
Yes	77 (23%)	1.2	-0.4, 2.9	0.126
Child perinatal exposure to tabacco up to one year
No	210 (65%)	—	—
Yes	112 (35%)	1.6	0.1, 3.0	0.034
Child perinatal passive smoking up to one year
No	217 (67%)	—	—		—	—		—	—
Yes	109 (33%)	1.6	0.2, 3.1	0.026	1.0	-0.5, 2.5	0.187	1.0	-0.5, 2.5	0.184
Maternal alcohol consumption during pregnancy
Did not drink	104 (31%)	—	—
Drank only before finding out she was pregnant	158 (48%)	-1.0	-2.5, 0.6	0.231
Drank	70 (21%)	0.1	-1.9, 2.0	0.953
Maternal alcohol consumption during pregnancy
Did not drink	104 (31%)	—	—
Drank only before finding out she was pregnant	158 (48%)	-1.0	-2.5, 0.6	0.231
<1drink/month when she knew she was pregnant	59 (18%)	-0.2	-2.2, 1.8	0.871
>1drink/month when she knew she was pregnant	11 (3.3%)	1.3	-2.7, 5.2	0.529
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	199 (63%)	—	—
Other	118 (37%)	-0.7	-2.2, 0.7	0.312
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	260 (82%)	—	—		—	—
Other	57 (18%)	-0.6	-2.4, 1.2	0.525	-0.6	-2.5, 1.3	0.555
Main mode of child care up to 1 year
Collective day care	266 (84%)	—	—					—	—
Other	51 (16%)	-0.4	-2.3, 1.5	0.694				-0.2	-2.2, 1.8	0.860
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	59 (19%)	—	—
Nursery assistant (out child home)	140 (44%)	0.4	-1.5, 2.3	0.683
Other	118 (37%)	-0.5	-2.4, 1.5	0.647
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	98 (31%)	—	—
Nursery assistant (out child home)	162 (51%)	0.1	-1.5, 1.7	0.912
Other	57 (18%)	-0.5	-2.6, 1.5	0.614
Main mode of child care up to 1 year
Collective day care	101 (32%)	—	—
Nursery assistant (out child home)	165 (52%)	-0.2	-1.8, 1.4	0.799
Other	51 (16%)	-0.5	-2.6, 1.6	0.642
Paternal education
≥5 years after graduation	152 (64%)	—	—
3-4 years after graduation	40 (17%)	1.3	-0.9, 3.5	0.244
2 years or less after graduation	46 (19%)	0.2	-1.9, 2.3	0.831
Paternal age at child birth (years)	301	-0.2	-0.3, 0.0	0.008
Paternal age at child birth
23-31 years	97 (32%)	—	—
32-36 years	105 (35%)	1.1	-0.6, 2.7	0.221
37-72 years	99 (33%)	-1.9	-3.6, -0.2	0.032
Child age at the CBCL 2 years evaluation	335	0.0	-0.3, 0.2	0.795
Child age at the CBCL 2 years evaluation					0.0	-0.3, 0.2	0.878	0.0	-0.3, 0.2	0.863
No. Obs.					335			335
R²					0.092			0.091
Adjusted R²					0.018			0.017
1 N; n (%)
2 CI = Confidence Interval

Figure 65: Multivariate model hypothesis checking (outcome is CBCL externe score Y2, before inclusion of microbiota variables)

SRS total score 3Y

Table 9:

Influence of maternal and child characteristics on the SRS total score at 3 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3321	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	332	2.1	-0.9, 5.1	0.174
Birth weight
<3 Kg	69 (21%)	—	—		—	—		—	—
3-3.4 Kg	163 (49%)	1.2	-2.5, 4.8	0.523	1.6	-2.6, 5.7	0.462	1.5	-2.6, 5.7	0.474
≥3.5 Kg	100 (30%)	2.3	-1.7, 6.3	0.254	3.0	-2.3, 8.3	0.271	2.9	-2.4, 8.2	0.279
Birth length (cm)	331	0.2	-0.5, 0.8	0.629
Birth length
<50 cm	121 (37%)	—	—		—	—		—	—
50-51 cm	132 (40%)	-0.3	-3.5, 2.9	0.854	-1.1	-4.8, 2.5	0.534	-1.1	-4.7, 2.5	0.538
≥52 cm	78 (24%)	1.1	-2.6, 4.8	0.557	-1.1	-6.0, 3.8	0.650	-1.1	-6.0, 3.8	0.664
Weight at one year (Kg)	328	0.3	-1.1, 1.6	0.692
Weight at one year
<8.5 Kg	57 (17%)	—	—
8.5-9.9 Kg	181 (55%)	0.6	-3.2, 4.4	0.759
≥10 Kg	90 (27%)	2.8	-1.5, 7.1	0.195
Length at one year (cm)	321	0.3	-0.2, 0.8	0.189
Length at one year
<75 cm	118 (37%)	—	—
75-77.9 cm	111 (35%)	-0.9	-4.2, 2.4	0.575
≥78 cm	92 (29%)	3.9	0.4, 7.3	0.029
Weight at 3 years (Kg)	307	0.4	-0.5, 1.3	0.367
Weight at 3 years
9-13 Kg	103 (34%)	—	—
14 Kg	104 (34%)	-1.8	-5.2, 1.7	0.316
15-20 Kg	100 (33%)	1.1	-2.4, 4.6	0.522
Length at 3 years (cm)	305	0.1	-0.3, 0.5	0.490
Length at 3 years
81-93 cm	94 (31%)	—	—
94-95 cm	106 (35%)	0.3	-3.2, 3.8	0.861
96-106 cm	105 (34%)	2.3	-1.3, 5.8	0.205
Child sex
Male	177 (53%)	—	—		—	—		—	—
Female	155 (47%)	-0.3	-3.1, 2.5	0.817	0.4	-2.4, 3.3	0.762	0.5	-2.4, 3.4	0.746
Maternal education
≥5 years after graduation	191 (58%)	—	—
3-4 years after graduation	90 (27%)	3.9	0.7, 7.1	0.018
2 years or less after graduation	49 (15%)	3.2	-0.8, 7.2	0.120
Maternal education
≥5 years after graduation	191 (58%)	—	—		—	—		—	—
<5 years after graduation	139 (42%)	3.7	0.8, 6.5	0.011	4.0	1.2, 6.8	0.005	4.0	1.2, 6.8	0.005
Maternal age at conception (years)	332	-0.3	-0.7, 0.1	0.105	-0.1	-0.5, 0.3	0.708	-0.1	-0.5, 0.3	0.721
Maternal BMI before pregnancy (kg/m2)	331	0.0	-0.4, 0.4	0.909
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	208 (63%)	1.2	-2.9, 5.4	0.561	2.0	-2.0, 6.0	0.325	2.0	-2.0, 6.0	0.329
≥24 Kg/m2	77 (23%)	1.3	-3.5, 6.0	0.599	1.7	-3.0, 6.3	0.474	1.7	-3.0, 6.3	0.482
Maternal parity
None	151 (45%)	—	—		—	—		—	—
1 child or more	181 (55%)	-4.7	-7.5, -2.0	<0.001	-6.5	-9.5, -3.6	<0.001	-6.5	-9.5, -3.6	<0.001
Breastfeeding duration
Not breastfed	25 (7.7%)	—	—		—	—		—	—
<24 weeks	113 (35%)	-3.2	-8.9, 2.4	0.263	-2.0	-7.4, 3.5	0.474	-2.0	-7.5, 3.4	0.466
24-47 weeks	112 (35%)	-3.9	-9.5, 1.8	0.182	-1.5	-7.0, 3.9	0.582	-1.6	-7.0, 3.9	0.577
Still breastfeed at 48 weeks	74 (23%)	-4.4	-10.4, 1.5	0.143	-2.8	-8.5, 2.9	0.335	-2.8	-8.6, 2.9	0.328
Gestational duration, completed weeks	332	0.6	-0.3, 1.5	0.188	0.4	-0.6, 1.4	0.388	0.4	-0.6, 1.4	0.383
Delivery mode
Vaginal delivery	278 (84%)	—	—		—	—		—	—
C-section	54 (16%)	1.1	-2.7, 4.8	0.583	-0.4	-4.2, 3.5	0.842	-0.4	-4.2, 3.5	0.848
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	238 (79%)	—	—		—	—		—	—
Between 6 and 12 months old	49 (16%)	0.6	-3.4, 4.5	0.784	-1.7	-5.8, 2.4	0.403	-1.7	-5.8, 2.3	0.401
Not introduced at 12 months old	15 (5.0%)	6.0	-0.8, 12.7	0.083	6.6	-0.3, 13.5	0.059	6.7	-0.2, 13.6	0.056
Presence of pets
No	211 (72%)	—	—		—	—		—	—
One or more	83 (28%)	0.1	-3.2, 3.4	0.944	-0.3	-3.9, 3.3	0.865	-0.3	-3.9, 3.3	0.865
Antibiotics use between 0-12 months old
No	228 (69%)	—	—		—	—		—	—
Yes	103 (31%)	-0.2	-3.2, 2.8	0.894	0.0	-3.0, 3.0	0.989	0.0	-3.0, 3.0	0.981
Learning materials score at 3 years of age (HOME questionnaire)	303	-1.3	-2.3, -0.2	0.019
Language stimulation score at 3 years of age (HOME questionnaire)	303	-1.8	-3.5, 0.0	0.052
Academic stimulation score at 3 years of age (HOME questionnaire)	303	-0.8	-2.5, 0.8	0.323
Variety score at 3 years of age (HOME questionnaire)	303	-1.2	-2.6, 0.1	0.062
HOME questionnaire total score	303	-0.8	-1.3, -0.3	0.004	-0.7	-1.2, -0.1	0.018	-0.7	-1.2, -0.1	0.018
Maternal anxiety score during the third trimester of pregnancy	323	0.6	0.1, 1.1	0.012
Maternal depression score during the third trimester of pregnancy	322	0.8	0.3, 1.3	0.002
Maternal anxiety and depression score during the third trimester of pregnancy	321	0.5	0.2, 0.8	<0.001	0.6	0.3, 1.0	<0.001	0.6	0.3, 0.9	<0.001
Maternal anxiety score when child is one year old	260	0.9	0.4, 1.4	<0.001
Maternal depression score when child is one year old	260	1.0	0.4, 1.5	<0.001
Maternal anxiety and depression score when child is one year old	260	0.7	0.4, 1.0	<0.001
Maternal active smoking during pregnancy
No	290 (94%)	—	—		—	—		—	—
Yes	19 (6.1%)	-1.0	-6.9, 4.9	0.737	-0.7	-7.0, 5.6	0.832	-0.7	-6.9, 5.6	0.833
Maternal passive smoking during pregnancy
No	261 (82%)	—	—
Yes	57 (18%)	-0.1	-3.8, 3.6	0.965
Child passive smoking during the first year of life
No	257 (77%)	—	—
Yes	75 (23%)	-0.2	-3.5, 3.1	0.900
Child perinatal exposure to tabacco up to one year
No	211 (67%)	—	—
Yes	106 (33%)	-0.6	-3.6, 2.4	0.689
Child perinatal passive smoking up to one year
No	218 (68%)	—	—		—	—		—	—
Yes	103 (32%)	-0.7	-3.7, 2.3	0.653	-1.7	-5.0, 1.5	0.300	-1.7	-5.0, 1.6	0.306
Maternal alcohol consumption during pregnancy
Did not drink	99 (30%)	—	—
Drank only before finding out she was pregnant	159 (48%)	-1.1	-4.3, 2.2	0.524
Drank	72 (22%)	-1.8	-5.7, 2.1	0.369
Maternal alcohol consumption during pregnancy
Did not drink	99 (30%)	—	—
Drank only before finding out she was pregnant	159 (48%)	-1.1	-4.3, 2.2	0.524
<1drink/month when she knew she was pregnant	61 (18%)	-2.1	-6.3, 2.0	0.310
>1drink/month when she knew she was pregnant	11 (3.3%)	0.1	-8.0, 8.2	0.982
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	198 (63%)	—	—
Other	117 (37%)	0.5	-2.4, 3.5	0.736
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	257 (82%)	—	—		—	—
Other	58 (18%)	-1.4	-5.1, 2.3	0.456	-0.9	-4.8, 2.9	0.625
Main mode of child care up to 1 year
Collective day care	264 (84%)	—	—					—	—
Other	51 (16%)	-1.6	-5.5, 2.2	0.407				-0.9	-4.8, 3.0	0.647
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	57 (18%)	—	—
Nursery assistant (out child home)	141 (45%)	4.4	0.4, 8.3	0.031
Other	117 (37%)	3.6	-0.5, 7.7	0.082
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	96 (30%)	—	—
Nursery assistant (out child home)	161 (51%)	1.6	-1.7, 4.8	0.345
Other	58 (18%)	-0.4	-4.6, 3.8	0.847
Main mode of child care up to 1 year
Collective day care	99 (31%)	—	—
Nursery assistant (out child home)	165 (52%)	1.9	-1.3, 5.1	0.237
Other	51 (16%)	-0.4	-4.8, 3.9	0.849
Paternal education
≥5 years after graduation	151 (64%)	—	—
3-4 years after graduation	41 (17%)	3.2	-1.4, 7.7	0.169
2 years or less after graduation	43 (18%)	1.4	-3.0, 5.8	0.539
Paternal age at child birth (years)	299	-0.3	-0.6, 0.0	0.052
Paternal age at child birth
23-31 years	97 (32%)	—	—
32-36 years	103 (34%)	-4.5	-8.1, -1.0	0.013
37-72 years	99 (33%)	-5.0	-8.6, -1.4	0.007
Child age at the SRS 3 years evaluation	332	0.3	0.0, 0.6	0.081
Child age at the SRS 3 years evaluation					0.2	-0.1, 0.5	0.280	0.2	-0.1, 0.5	0.284
No. Obs.					332			332
R²					0.171			0.171
Adjusted R²					0.104			0.103
1 N; n (%)
2 CI = Confidence Interval

Figure 66: Multivariate model hypothesis checking (outcome is SRS total score Y3, before inclusion of microbiota variables)

BRIEF-P Y3

Inhibit score Y3

Table 10:

Influence of maternal and child characteristics on the BRIEF-P inhibit score at 2 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3301	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	330	0.2	-1.0, 1.4	0.704
Birth weight
<3 Kg	68 (21%)	—	—		—	—		—	—
3-3.4 Kg	161 (49%)	0.1	-1.4, 1.5	0.931	-0.5	-2.2, 1.3	0.607	-0.5	-2.3, 1.2	0.559
≥3.5 Kg	101 (31%)	0.0	-1.6, 1.6	0.993	-1.2	-3.4, 1.0	0.297	-1.2	-3.5, 1.0	0.272
Birth length (cm)	329	0.1	-0.2, 0.3	0.508
Birth length
<50 cm	118 (36%)	—	—		—	—		—	—
50-51 cm	131 (40%)	0.8	-0.5, 2.1	0.230	1.1	-0.5, 2.6	0.171	1.1	-0.5, 2.6	0.175
≥52 cm	80 (24%)	1.3	-0.1, 2.8	0.074	2.0	0.0, 4.0	0.055	2.0	0.0, 4.0	0.050
Weight at one year (Kg)	326	0.3	-0.3, 0.8	0.330
Weight at one year
<8.5 Kg	55 (17%)	—	—
8.5-9.9 Kg	179 (55%)	1.3	-0.3, 2.8	0.114
≥10 Kg	92 (28%)	2.0	0.3, 3.7	0.021
Length at one year (cm)	319	0.2	0.0, 0.4	0.065
Length at one year
<75 cm	116 (36%)	—	—
75-77.9 cm	112 (35%)	0.6	-0.7, 2.0	0.340
≥78 cm	91 (29%)	2.0	0.6, 3.4	0.005
Weight at 3 years (Kg)	305	0.4	0.0, 0.7	0.034
Weight at 3 years
9-13 Kg	102 (33%)	—	—
14 Kg	103 (34%)	0.1	-1.3, 1.5	0.882
15-20 Kg	100 (33%)	1.3	-0.1, 2.7	0.073
Length at 3 years (cm)	303	0.2	0.0, 0.4	0.010
Length at 3 years
81-93 cm	93 (31%)	—	—
94-95 cm	104 (34%)	1.3	-0.1, 2.7	0.070
96-106 cm	106 (35%)	1.9	0.5, 3.3	0.009
Child sex
Male	175 (53%)	—	—		—	—		—	—
Female	155 (47%)	-1.2	-2.3, 0.0	0.042	-0.7	-1.9, 0.5	0.237	-0.7	-2.0, 0.5	0.228
Maternal education
≥5 years after graduation	190 (58%)	—	—
3-4 years after graduation	89 (27%)	0.7	-0.6, 2.0	0.276
2 years or less after graduation	49 (15%)	1.0	-0.6, 2.6	0.217
Maternal education
≥5 years after graduation	190 (58%)	—	—		—	—		—	—
<5 years after graduation	138 (42%)	0.8	-0.3, 1.9	0.151	0.8	-0.4, 2.0	0.189	0.8	-0.4, 1.9	0.201
Maternal age at conception (years)	330	-0.1	-0.2, 0.0	0.191	-0.1	-0.2, 0.1	0.488	-0.1	-0.2, 0.1	0.473
Maternal BMI before pregnancy (kg/m2)	329	0.0	-0.1, 0.2	0.725
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	208 (63%)	0.9	-0.8, 2.5	0.309	0.8	-0.8, 2.5	0.321	0.9	-0.8, 2.6	0.303
≥24 Kg/m2	75 (23%)	0.7	-1.2, 2.6	0.493	0.6	-1.3, 2.6	0.536	0.6	-1.3, 2.5	0.545
Maternal parity
None	148 (45%)	—	—		—	—		—	—
1 child or more	182 (55%)	-1.0	-2.1, 0.1	0.083	-1.5	-2.7, -0.2	0.021	-1.5	-2.8, -0.3	0.018
Breastfeeding duration
Not breastfed	24 (7.5%)	—	—		—	—		—	—
<24 weeks	114 (35%)	-0.3	-2.5, 2.0	0.813	0.1	-2.2, 2.4	0.936	0.1	-2.2, 2.5	0.907
24-47 weeks	109 (34%)	-0.3	-2.5, 2.0	0.829	0.6	-1.8, 3.0	0.627	0.6	-1.8, 3.0	0.602
Still breastfeed at 48 weeks	75 (23%)	0.4	-2.0, 2.7	0.760	1.1	-1.3, 3.5	0.382	1.1	-1.4, 3.5	0.391
Gestational duration, completed weeks	330	0.0	-0.4, 0.3	0.790	-0.1	-0.5, 0.3	0.690	-0.1	-0.5, 0.4	0.738
Delivery mode
Vaginal delivery	276 (84%)	—	—		—	—		—	—
C-section	54 (16%)	0.5	-1.0, 2.0	0.505	0.0	-1.6, 1.7	0.958	0.1	-1.5, 1.7	0.901
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	236 (79%)	—	—		—	—		—	—
Between 6 and 12 months old	48 (16%)	0.1	-1.5, 1.7	0.933	-0.6	-2.3, 1.0	0.461	-0.6	-2.3, 1.0	0.445
Not introduced at 12 months old	15 (5.0%)	2.2	-0.4, 4.9	0.102	1.8	-1.0, 4.6	0.205	1.7	-1.0, 4.5	0.218
Presence of pets
No	209 (72%)	—	—		—	—		—	—
One or more	83 (28%)	0.3	-1.0, 1.6	0.625	0.1	-1.3, 1.6	0.878	0.1	-1.4, 1.5	0.915
Antibiotics use between 0-12 months old
No	229 (70%)	—	—		—	—		—	—
Yes	100 (30%)	-0.2	-1.4, 1.0	0.793	0.0	-1.2, 1.3	0.958	0.0	-1.2, 1.3	0.965
Learning materials score at 3 years of age (HOME questionnaire)	301	0.0	-0.5, 0.4	0.880
Language stimulation score at 3 years of age (HOME questionnaire)	301	-0.2	-0.9, 0.5	0.614
Academic stimulation score at 3 years of age (HOME questionnaire)	301	0.1	-0.6, 0.7	0.861
Variety score at 3 years of age (HOME questionnaire)	301	-0.4	-0.9, 0.1	0.144
HOME questionnaire total score	301	-0.1	-0.3, 0.1	0.442	-0.1	-0.3, 0.2	0.538	-0.1	-0.3, 0.2	0.522
Maternal anxiety score during the third trimester of pregnancy	321	0.2	0.0, 0.4	0.069
Maternal depression score during the third trimester of pregnancy	321	0.2	0.0, 0.4	0.023
Maternal anxiety and depression score during the third trimester of pregnancy	320	0.1	0.0, 0.3	0.014	0.2	0.0, 0.3	0.017	0.2	0.0, 0.3	0.019
Maternal anxiety score when child is one year old	258	0.1	-0.1, 0.3	0.230
Maternal depression score when child is one year old	258	0.3	0.1, 0.5	0.008
Maternal anxiety and depression score when child is one year old	258	0.2	0.0, 0.3	0.022
Maternal active smoking during pregnancy
No	288 (94%)	—	—		—	—		—	—
Yes	19 (6.2%)	0.5	-1.9, 2.9	0.680	-0.1	-2.7, 2.5	0.943	-0.1	-2.7, 2.5	0.957
Maternal passive smoking during pregnancy
No	259 (82%)	—	—
Yes	57 (18%)	-0.1	-1.6, 1.4	0.914
Child passive smoking during the first year of life
No	256 (78%)	—	—
Yes	74 (22%)	0.2	-1.1, 1.6	0.715
Child perinatal exposure to tabacco up to one year
No	209 (66%)	—	—
Yes	106 (34%)	0.5	-0.7, 1.7	0.429
Child perinatal passive smoking up to one year
No	216 (68%)	—	—		—	—		—	—
Yes	103 (32%)	0.5	-0.7, 1.7	0.411	0.3	-1.1, 1.7	0.667	0.3	-1.1, 1.7	0.653
Maternal alcohol consumption during pregnancy
Did not drink	99 (30%)	—	—
Drank only before finding out she was pregnant	157 (48%)	-0.3	-1.6, 1.0	0.639
Drank	72 (22%)	-0.9	-2.5, 0.7	0.251
Maternal alcohol consumption during pregnancy
Did not drink	99 (30%)	—	—
Drank only before finding out she was pregnant	157 (48%)	-0.3	-1.6, 1.0	0.639
<1drink/month when she knew she was pregnant	61 (19%)	-1.0	-2.6, 0.7	0.242
>1drink/month when she knew she was pregnant	11 (3.4%)	-0.6	-3.8, 2.7	0.735
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	194 (62%)	—	—
Other	118 (38%)	-0.1	-1.3, 1.1	0.830
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	255 (82%)	—	—		—	—
Other	57 (18%)	-0.6	-2.1, 0.9	0.449	-0.5	-2.1, 1.0	0.497
Main mode of child care up to 1 year
Collective day care	262 (84%)	—	—					—	—
Other	50 (16%)	-0.2	-1.7, 1.4	0.823				0.0	-1.7, 1.7	>0.999
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	56 (18%)	—	—
Nursery assistant (out child home)	138 (44%)	1.2	-0.4, 2.8	0.144
Other	118 (38%)	0.7	-0.9, 2.4	0.389
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	95 (30%)	—	—
Nursery assistant (out child home)	160 (51%)	0.8	-0.6, 2.1	0.258
Other	57 (18%)	-0.1	-1.8, 1.6	0.910
Main mode of child care up to 1 year
Collective day care	98 (31%)	—	—
Nursery assistant (out child home)	164 (53%)	0.7	-0.6, 2.0	0.320
Other	50 (16%)	0.2	-1.5, 2.0	0.796
Paternal education
≥5 years after graduation	149 (64%)	—	—
3-4 years after graduation	41 (18%)	-0.2	-2.0, 1.6	0.829
2 years or less after graduation	44 (19%)	0.8	-0.9, 2.5	0.355
Paternal age at child birth (years)	296	-0.1	-0.2, 0.1	0.295
Paternal age at child birth
23-31 years	97 (33%)	—	—
32-36 years	98 (33%)	-1.4	-2.8, 0.1	0.063
37-72 years	101 (34%)	-1.5	-3.0, -0.1	0.034
Child age at the SRS 3 years evaluation	330	0.1	0.0, 0.2	0.076
Child age at the SRS 3 years evaluation					0.1	0.0, 0.2	0.119	0.1	0.0, 0.2	0.122
No. Obs.					330			330
R²					0.097			0.095
Adjusted R²					0.022			0.021
1 N; n (%)
2 CI = Confidence Interval

Figure 67: Multivariate model hypothesis checking (outcome is BRIEF-P inhibit score Y3, before inclusion of microbiota variables)

Shift score Y3

Table 11:

Influence of maternal and child characteristics on the BRIEF-P shift score at 2 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3381	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	338	0.5	-0.2, 1.2	0.178
Birth weight
<3 Kg	70 (21%)	—	—		—	—		—	—
3-3.4 Kg	166 (49%)	0.2	-0.7, 1.0	0.703	-0.2	-1.2, 0.8	0.736	-0.1	-1.1, 0.9	0.839
≥3.5 Kg	102 (30%)	0.6	-0.3, 1.5	0.218	0.3	-1.0, 1.6	0.629	0.4	-0.9, 1.6	0.548
Birth length (cm)	337	0.1	-0.1, 0.2	0.399
Birth length
<50 cm	121 (36%)	—	—		—	—		—	—
50-51 cm	135 (40%)	0.4	-0.4, 1.1	0.312	0.2	-0.6, 1.1	0.583	0.2	-0.6, 1.1	0.602
≥52 cm	81 (24%)	0.3	-0.5, 1.2	0.420	0.3	-0.9, 1.4	0.656	0.2	-1.0, 1.4	0.735
Weight at one year (Kg)	334	0.1	-0.2, 0.4	0.713
Weight at one year
<8.5 Kg	58 (17%)	—	—
8.5-9.9 Kg	182 (54%)	-0.3	-1.1, 0.6	0.559
≥10 Kg	94 (28%)	0.4	-0.5, 1.4	0.362
Length at one year (cm)	327	0.1	0.0, 0.2	0.223
Length at one year
<75 cm	119 (36%)	—	—
75-77.9 cm	116 (35%)	0.1	-0.6, 0.8	0.781
≥78 cm	92 (28%)	0.6	-0.2, 1.4	0.119
Weight at 3 years (Kg)	313	-0.1	-0.3, 0.1	0.566
Weight at 3 years
9-13 Kg	105 (34%)	—	—
14 Kg	104 (33%)	-0.4	-1.2, 0.4	0.322
15-20 Kg	104 (33%)	-0.2	-1.0, 0.6	0.641
Length at 3 years (cm)	311	0.0	-0.1, 0.1	0.494
Length at 3 years
81-93 cm	95 (31%)	—	—
94-95 cm	109 (35%)	0.2	-0.6, 1.0	0.599
96-106 cm	107 (34%)	0.3	-0.5, 1.1	0.420
Child sex
Male	181 (54%)	—	—		—	—		—	—
Female	157 (46%)	0.1	-0.5, 0.7	0.721	0.3	-0.4, 0.9	0.467	0.2	-0.5, 0.9	0.512
Maternal education
≥5 years after graduation	195 (58%)	—	—
3-4 years after graduation	90 (27%)	0.2	-0.6, 0.9	0.623
2 years or less after graduation	51 (15%)	0.4	-0.5, 1.3	0.379
Maternal education
≥5 years after graduation	195 (58%)	—	—		—	—		—	—
<5 years after graduation	141 (42%)	0.3	-0.4, 0.9	0.415	0.4	-0.3, 1.1	0.223	0.4	-0.3, 1.1	0.246
Maternal age at conception (years)	338	0.0	-0.1, 0.0	0.381	0.0	-0.1, 0.0	0.297	0.0	-0.1, 0.0	0.283
Maternal BMI before pregnancy (kg/m2)	337	0.0	-0.1, 0.0	0.302
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	213 (63%)	-0.5	-1.5, 0.4	0.257	-0.3	-1.3, 0.6	0.492	-0.3	-1.3, 0.6	0.496
≥24 Kg/m2	78 (23%)	-0.6	-1.7, 0.4	0.240	-0.6	-1.7, 0.5	0.251	-0.6	-1.7, 0.5	0.275
Maternal parity
None	154 (46%)	—	—		—	—		—	—
1 child or more	184 (54%)	-0.5	-1.2, 0.1	0.099	-0.8	-1.5, -0.1	0.023	-0.8	-1.5, -0.1	0.026
Breastfeeding duration
Not breastfed	26 (7.9%)	—	—		—	—		—	—
<24 weeks	115 (35%)	0.4	-0.9, 1.7	0.546	0.7	-0.5, 2.0	0.266	0.7	-0.5, 2.0	0.251
24-47 weeks	112 (34%)	1.1	-0.2, 2.3	0.099	1.5	0.2, 2.8	0.021	1.5	0.2, 2.8	0.021
Still breastfeed at 48 weeks	77 (23%)	0.9	-0.4, 2.2	0.185	1.1	-0.2, 2.5	0.094	1.2	-0.2, 2.5	0.086
Gestational duration, completed weeks	338	0.1	-0.1, 0.3	0.357	0.1	-0.2, 0.3	0.562	0.1	-0.2, 0.3	0.610
Delivery mode
Vaginal delivery	282 (83%)	—	—		—	—		—	—
C-section	56 (17%)	0.2	-0.6, 1.1	0.577	0.2	-0.7, 1.1	0.608	0.2	-0.7, 1.1	0.659
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	243 (79%)	—	—		—	—		—	—
Between 6 and 12 months old	49 (16%)	0.0	-0.9, 0.9	0.975	-0.6	-1.5, 0.3	0.205	-0.6	-1.5, 0.3	0.218
Not introduced at 12 months old	15 (4.9%)	-0.1	-1.6, 1.4	0.902	0.0	-1.7, 1.7	0.998	0.0	-1.8, 1.7	0.961
Presence of pets
No	215 (72%)	—	—		—	—		—	—
One or more	84 (28%)	-0.2	-1.0, 0.5	0.562	-0.4	-1.3, 0.4	0.326	-0.4	-1.3, 0.4	0.336
Antibiotics use between 0-12 months old
No	232 (69%)	—	—		—	—		—	—
Yes	105 (31%)	-0.1	-0.8, 0.6	0.756	-0.1	-0.8, 0.6	0.822	-0.1	-0.8, 0.6	0.851
Learning materials score at 3 years of age (HOME questionnaire)	309	0.0	-0.3, 0.2	0.798
Language stimulation score at 3 years of age (HOME questionnaire)	309	-0.3	-0.7, 0.1	0.143
Academic stimulation score at 3 years of age (HOME questionnaire)	309	0.1	-0.3, 0.4	0.711
Variety score at 3 years of age (HOME questionnaire)	309	0.0	-0.3, 0.3	0.903
HOME questionnaire total score	309	0.0	-0.1, 0.1	0.688	0.0	-0.1, 0.1	0.983	0.0	-0.1, 0.1	>0.999
Maternal anxiety score during the third trimester of pregnancy	329	0.1	0.0, 0.3	0.009
Maternal depression score during the third trimester of pregnancy	328	0.1	0.0, 0.2	0.186
Maternal anxiety and depression score during the third trimester of pregnancy	327	0.1	0.0, 0.2	0.014	0.1	0.0, 0.2	0.004	0.1	0.0, 0.2	0.002
Maternal anxiety score when child is one year old	265	0.2	0.1, 0.3	<0.001
Maternal depression score when child is one year old	265	0.2	0.1, 0.4	<0.001
Maternal anxiety and depression score when child is one year old	265	0.2	0.1, 0.2	<0.001
Maternal active smoking during pregnancy
No	295 (94%)	—	—		—	—		—	—
Yes	19 (6.1%)	-0.6	-1.9, 0.7	0.348	-0.3	-2.7, 2.0	0.753	-0.3	-2.7, 2.0	0.751
Maternal passive smoking during pregnancy
No	266 (82%)	—	—
Yes	57 (18%)	-0.1	-0.9, 0.7	0.786
Child passive smoking during the first year of life
No	262 (78%)	—	—
Yes	76 (22%)	-0.2	-0.9, 0.6	0.691
Child perinatal exposure to tabacco up to one year
No	214 (66%)	—	—
Yes	108 (34%)	0.0	-0.7, 0.6	0.921
Child perinatal passive smoking up to one year
No	221 (68%)	—	—		—	—		—	—
Yes	105 (32%)	0.0	-0.7, 0.7	0.996	-0.1	-0.9, 0.7	0.839	-0.1	-0.9, 0.7	0.778
Maternal alcohol consumption during pregnancy
Did not drink	102 (30%)	—	—
Drank only before finding out she was pregnant	162 (48%)	-0.4	-1.2, 0.3	0.237
Drank	72 (21%)	-0.8	-1.7, 0.1	0.091
Maternal alcohol consumption during pregnancy
Did not drink	102 (30%)	—	—
Drank only before finding out she was pregnant	162 (48%)	-0.4	-1.2, 0.3	0.237
<1drink/month when she knew she was pregnant	61 (18%)	-0.9	-1.8, 0.1	0.074
>1drink/month when she knew she was pregnant	11 (3.3%)	-0.3	-2.1, 1.5	0.754
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	201 (63%)	—	—
Other	119 (37%)	0.8	0.1, 1.4	0.020
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	263 (82%)	—	—		—	—
Other	57 (18%)	0.9	0.0, 1.7	0.045	1.0	0.1, 1.9	0.027
Main mode of child care up to 1 year
Collective day care	270 (84%)	—	—					—	—
Other	50 (16%)	0.7	-0.2, 1.6	0.129				0.8	-0.1, 1.8	0.096
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	58 (18%)	—	—
Nursery assistant (out child home)	143 (45%)	0.2	-0.7, 1.1	0.620
Other	119 (37%)	0.9	0.0, 1.9	0.043
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	98 (31%)	—	—
Nursery assistant (out child home)	165 (52%)	0.3	-0.4, 1.0	0.411
Other	57 (18%)	1.0	0.1, 2.0	0.032
Main mode of child care up to 1 year
Collective day care	101 (32%)	—	—
Nursery assistant (out child home)	169 (53%)	0.4	-0.3, 1.1	0.308
Other	50 (16%)	0.9	-0.1, 1.9	0.069
Paternal education
≥5 years after graduation	152 (64%)	—	—
3-4 years after graduation	41 (17%)	0.1	-1.0, 1.1	0.902
2 years or less after graduation	45 (19%)	0.2	-0.8, 1.2	0.688
Paternal age at child birth (years)	303	0.0	-0.1, 0.0	0.338
Paternal age at child birth
23-31 years	99 (33%)	—	—
32-36 years	102 (34%)	-0.9	-1.7, -0.1	0.028
37-72 years	102 (34%)	-0.3	-1.1, 0.5	0.437
Child age at the SRS 3 years evaluation	338	0.0	0.0, 0.1	0.324
Child age at the SRS 3 years evaluation					0.0	0.0, 0.1	0.308	0.0	0.0, 0.1	0.291
No. Obs.					338			338
R²					0.098			0.092
Adjusted R²					0.026			0.019
1 N; n (%)
2 CI = Confidence Interval

Figure 68: Multivariate model hypothesis checking (outcome is BRIEF-P shift score Y3, before inclusion of microbiota variables)

Emotional control score Y3

Table 12:

Influence of maternal and child characteristics on the BRIEF-P emotional control score at 2 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3371	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	337	0.2	-0.6, 1.0	0.667
Birth weight
<3 Kg	70 (21%)	—	—		—	—		—	—
3-3.4 Kg	165 (49%)	0.2	-0.8, 1.2	0.707	0.0	-1.2, 1.1	0.945	0.0	-1.2, 1.2	0.972
≥3.5 Kg	102 (30%)	0.4	-0.7, 1.4	0.506	0.2	-1.3, 1.7	0.817	0.2	-1.3, 1.7	0.797
Birth length (cm)	336	0.0	-0.2, 0.1	0.763
Birth length
<50 cm	121 (36%)	—	—		—	—		—	—
50-51 cm	134 (40%)	0.3	-0.6, 1.1	0.525	0.2	-0.8, 1.2	0.706	0.2	-0.8, 1.2	0.698
≥52 cm	81 (24%)	0.4	-0.6, 1.3	0.463	0.3	-1.0, 1.7	0.632	0.3	-1.0, 1.7	0.638
Weight at one year (Kg)	333	0.0	-0.3, 0.4	0.789
Weight at one year
<8.5 Kg	58 (17%)	—	—
8.5-9.9 Kg	182 (55%)	0.7	-0.4, 1.7	0.204
≥10 Kg	93 (28%)	0.8	-0.3, 1.9	0.166
Length at one year (cm)	326	0.0	-0.1, 0.2	0.502
Length at one year
<75 cm	119 (37%)	—	—
75-77.9 cm	116 (36%)	0.4	-0.5, 1.3	0.364
≥78 cm	91 (28%)	0.6	-0.3, 1.6	0.192
Weight at 3 years (Kg)	312	0.1	-0.2, 0.3	0.620
Weight at 3 years
9-13 Kg	105 (34%)	—	—
14 Kg	104 (33%)	0.0	-1.0, 0.9	0.942
15-20 Kg	103 (33%)	0.4	-0.6, 1.3	0.444
Length at 3 years (cm)	310	0.1	0.0, 0.2	0.234
Length at 3 years
81-93 cm	95 (31%)	—	—
94-95 cm	108 (35%)	0.5	-0.5, 1.4	0.337
96-106 cm	107 (35%)	0.6	-0.4, 1.5	0.236
Child sex
Male	180 (53%)	—	—		—	—		—	—
Female	157 (47%)	0.0	-0.8, 0.7	0.925	0.2	-0.6, 1.0	0.636	0.2	-0.6, 1.0	0.617
Maternal education
≥5 years after graduation	194 (58%)	—	—
3-4 years after graduation	90 (27%)	0.7	-0.1, 1.6	0.098
2 years or less after graduation	51 (15%)	-0.2	-1.3, 0.9	0.724
Maternal education
≥5 years after graduation	194 (58%)	—	—		—	—		—	—
<5 years after graduation	141 (42%)	0.4	-0.4, 1.1	0.300	0.4	-0.4, 1.2	0.283	0.4	-0.3, 1.2	0.271
Maternal age at conception (years)	337	-0.1	-0.2, 0.0	0.048	-0.1	-0.2, 0.0	0.166	-0.1	-0.2, 0.0	0.175
Maternal BMI before pregnancy (kg/m2)	336	0.0	-0.1, 0.1	0.863
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	212 (63%)	0.5	-0.6, 1.6	0.381	0.7	-0.4, 1.8	0.211	0.7	-0.4, 1.8	0.223
≥24 Kg/m2	78 (23%)	0.2	-1.1, 1.5	0.746	0.3	-1.0, 1.6	0.699	0.3	-1.0, 1.6	0.701
Maternal parity
None	153 (45%)	—	—		—	—		—	—
1 child or more	184 (55%)	-0.9	-1.6, -0.2	0.016	-1.2	-2.0, -0.3	0.007	-1.1	-2.0, -0.3	0.008
Breastfeeding duration
Not breastfed	26 (7.9%)	—	—		—	—		—	—
<24 weeks	115 (35%)	-0.1	-1.6, 1.3	0.846	0.1	-1.4, 1.6	0.927	0.0	-1.5, 1.6	0.949
24-47 weeks	111 (34%)	0.5	-1.0, 2.0	0.493	1.0	-0.6, 2.5	0.217	0.9	-0.6, 2.5	0.228
Still breastfeed at 48 weeks	77 (23%)	0.7	-0.9, 2.2	0.379	1.0	-0.6, 2.6	0.218	1.0	-0.6, 2.6	0.215
Gestational duration, completed weeks	337	0.1	-0.1, 0.3	0.475	0.1	-0.2, 0.3	0.675	0.1	-0.2, 0.3	0.703
Delivery mode
Vaginal delivery	282 (84%)	—	—		—	—		—	—
C-section	55 (16%)	0.2	-0.8, 1.2	0.767	0.0	-1.0, 1.1	0.945	0.0	-1.0, 1.1	0.978
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	243 (79%)	—	—		—	—		—	—
Between 6 and 12 months old	48 (16%)	-0.1	-1.2, 0.9	0.786	-0.4	-1.6, 0.7	0.476	-0.4	-1.6, 0.8	0.488
Not introduced at 12 months old	15 (4.9%)	1.1	-0.7, 2.9	0.236	1.3	-0.6, 3.2	0.175	1.4	-0.6, 3.3	0.165
Presence of pets
No	215 (72%)	—	—		—	—		—	—
One or more	84 (28%)	0.4	-0.4, 1.3	0.305	0.2	-0.8, 1.1	0.746	0.2	-0.8, 1.1	0.723
Antibiotics use between 0-12 months old
No	232 (69%)	—	—		—	—		—	—
Yes	104 (31%)	-0.1	-0.9, 0.7	0.835	0.1	-0.8, 0.9	0.849	0.1	-0.8, 0.9	0.852
Learning materials score at 3 years of age (HOME questionnaire)	308	-0.1	-0.4, 0.2	0.581
Language stimulation score at 3 years of age (HOME questionnaire)	308	-0.4	-0.8, 0.1	0.102
Academic stimulation score at 3 years of age (HOME questionnaire)	308	0.1	-0.3, 0.5	0.667
Variety score at 3 years of age (HOME questionnaire)	308	-0.1	-0.4, 0.3	0.738
HOME questionnaire total score	308	-0.1	-0.2, 0.1	0.440	0.0	-0.2, 0.1	0.633	0.0	-0.2, 0.1	0.640
Maternal anxiety score during the third trimester of pregnancy	328	0.1	0.0, 0.3	0.036
Maternal depression score during the third trimester of pregnancy	328	0.1	-0.1, 0.2	0.218
Maternal anxiety and depression score during the third trimester of pregnancy	327	0.1	0.0, 0.2	0.037	0.1	0.0, 0.2	0.008	0.1	0.0, 0.2	0.007
Maternal anxiety score when child is one year old	265	0.2	0.0, 0.3	0.020
Maternal depression score when child is one year old	265	0.3	0.1, 0.4	<0.001
Maternal anxiety and depression score when child is one year old	265	0.2	0.1, 0.2	<0.001
Maternal active smoking during pregnancy
No	295 (94%)	—	—		—	—		—	—
Yes	19 (6.1%)	0.0	-1.6, 1.6	0.997	0.1	-2.0, 2.3	0.893	0.1	-2.0, 2.2	0.901
Maternal passive smoking during pregnancy
No	266 (82%)	—	—
Yes	57 (18%)	0.2	-0.8, 1.2	0.674
Child passive smoking during the first year of life
No	261 (77%)	—	—
Yes	76 (23%)	0.2	-0.7, 1.1	0.646
Child perinatal exposure to tabacco up to one year
No	214 (66%)	—	—
Yes	108 (34%)	0.2	-0.5, 1.0	0.544
Child perinatal passive smoking up to one year
No	221 (68%)	—	—		—	—		—	—
Yes	105 (32%)	0.3	-0.5, 1.1	0.455	0.1	-0.8, 0.9	0.850	0.1	-0.8, 0.9	0.849
Maternal alcohol consumption during pregnancy
Did not drink	101 (30%)	—	—
Drank only before finding out she was pregnant	162 (48%)	0.1	-0.8, 0.9	0.869
Drank	72 (21%)	-0.5	-1.5, 0.6	0.397
Maternal alcohol consumption during pregnancy
Did not drink	101 (30%)	—	—
Drank only before finding out she was pregnant	162 (48%)	0.1	-0.8, 0.9	0.869
<1drink/month when she knew she was pregnant	61 (18%)	-0.4	-1.5, 0.7	0.459
>1drink/month when she knew she was pregnant	11 (3.3%)	-0.7	-2.8, 1.5	0.552
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	200 (63%)	—	—
Other	119 (37%)	0.0	-0.8, 0.8	0.961
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	262 (82%)	—	—		—	—
Other	57 (18%)	0.0	-1.0, 1.0	0.979	0.1	-0.9, 1.2	0.809
Main mode of child care up to 1 year
Collective day care	269 (84%)	—	—					—	—
Other	50 (16%)	-0.3	-1.3, 0.8	0.624				-0.1	-1.2, 1.0	0.830
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	58 (18%)	—	—
Nursery assistant (out child home)	142 (45%)	1.1	0.0, 2.2	0.046
Other	119 (37%)	0.8	-0.3, 1.8	0.179
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	98 (31%)	—	—
Nursery assistant (out child home)	164 (51%)	0.7	-0.2, 1.6	0.115
Other	57 (18%)	0.4	-0.7, 1.6	0.463
Main mode of child care up to 1 year
Collective day care	101 (32%)	—	—
Nursery assistant (out child home)	168 (53%)	0.6	-0.3, 1.5	0.182
Other	50 (16%)	0.1	-1.1, 1.3	0.865
Paternal education
≥5 years after graduation	152 (64%)	—	—
3-4 years after graduation	41 (17%)	0.3	-0.9, 1.5	0.629
2 years or less after graduation	45 (19%)	0.2	-0.9, 1.4	0.686
Paternal age at child birth (years)	302	-0.1	-0.2, 0.0	0.006
Paternal age at child birth
23-31 years	99 (33%)	—	—
32-36 years	101 (33%)	-1.3	-2.3, -0.4	0.007
37-72 years	102 (34%)	-1.5	-2.5, -0.6	0.002
Child age at the SRS 3 years evaluation	337	0.0	-0.1, 0.1	0.923
Child age at the SRS 3 years evaluation					0.0	-0.1, 0.1	0.802	0.0	-0.1, 0.1	0.801
No. Obs.					337			337
R²					0.087			0.087
Adjusted R²					0.013			0.013
1 N; n (%)
2 CI = Confidence Interval

Figure 69: Multivariate model hypothesis checking (outcome is BRIEF-P emotional control score Y3, before inclusion of microbiota variables)

Working memory score Y3

Table 13:

Influence of maternal and child characteristics on the BRIEF-P working memory score at 2 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3291	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	329	0.1	-0.9, 1.1	0.843
Birth weight
<3 Kg	69 (21%)	—	—		—	—		—	—
3-3.4 Kg	162 (49%)	-1.0	-2.2, 0.2	0.114	-1.4	-2.9, 0.1	0.061	-1.5	-2.9, 0.0	0.050
≥3.5 Kg	98 (30%)	-0.5	-1.8, 0.8	0.468	-0.7	-2.6, 1.1	0.437	-0.8	-2.7, 1.1	0.400
Birth length (cm)	328	-0.1	-0.3, 0.1	0.332
Birth length
<50 cm	118 (36%)	—	—		—	—		—	—
50-51 cm	131 (40%)	-0.1	-1.2, 1.0	0.848	-0.2	-1.5, 1.0	0.720	-0.2	-1.5, 1.0	0.711
≥52 cm	79 (24%)	-0.2	-1.4, 1.1	0.808	-0.5	-2.2, 1.2	0.568	-0.5	-2.2, 1.2	0.596
Weight at one year (Kg)	325	-0.1	-0.6, 0.3	0.631
Weight at one year
<8.5 Kg	56 (17%)	—	—
8.5-9.9 Kg	177 (54%)	0.1	-1.2, 1.5	0.831
≥10 Kg	92 (28%)	0.7	-0.7, 2.2	0.332
Length at one year (cm)	318	0.0	-0.2, 0.1	0.648
Length at one year
<75 cm	117 (37%)	—	—
75-77.9 cm	111 (35%)	-0.8	-2.0, 0.3	0.148
≥78 cm	90 (28%)	0.5	-0.7, 1.7	0.404
Weight at 3 years (Kg)	304	0.1	-0.2, 0.4	0.576
Weight at 3 years
9-13 Kg	102 (34%)	—	—
14 Kg	99 (33%)	0.3	-0.9, 1.5	0.639
15-20 Kg	103 (34%)	0.6	-0.6, 1.8	0.316
Length at 3 years (cm)	302	0.0	-0.1, 0.1	0.906
Length at 3 years
81-93 cm	92 (30%)	—	—
94-95 cm	107 (35%)	-0.6	-1.8, 0.5	0.289
96-106 cm	103 (34%)	0.3	-0.9, 1.5	0.578
Child sex
Male	177 (54%)	—	—		—	—		—	—
Female	152 (46%)	-0.1	-1.0, 0.9	0.908	-0.2	-1.2, 0.8	0.738	-0.2	-1.2, 0.8	0.734
Maternal education
≥5 years after graduation	192 (59%)	—	—
3-4 years after graduation	87 (27%)	0.9	-0.2, 2.0	0.102
2 years or less after graduation	48 (15%)	0.7	-0.7, 2.1	0.320
Maternal education
≥5 years after graduation	192 (59%)	—	—		—	—		—	—
<5 years after graduation	135 (41%)	0.8	-0.1, 1.8	0.085	0.9	0.0, 1.9	0.061	0.9	0.0, 1.9	0.062
Maternal age at conception (years)	329	0.0	-0.2, 0.1	0.553	0.0	-0.1, 0.1	0.865	0.0	-0.1, 0.1	0.856
Maternal BMI before pregnancy (kg/m2)	328	0.0	-0.2, 0.1	0.478
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	207 (63%)	0.7	-0.7, 2.1	0.341	0.9	-0.5, 2.4	0.192	1.0	-0.4, 2.4	0.179
≥24 Kg/m2	76 (23%)	-0.3	-1.9, 1.3	0.705	-0.1	-1.7, 1.5	0.915	-0.1	-1.7, 1.5	0.902
Maternal parity
None	152 (46%)	—	—		—	—		—	—
1 child or more	177 (54%)	-1.2	-2.1, -0.3	0.012	-1.4	-2.4, -0.3	0.009	-1.4	-2.5, -0.4	0.007
Breastfeeding duration
Not breastfed	25 (7.8%)	—	—		—	—		—	—
<24 weeks	113 (35%)	0.5	-1.5, 2.4	0.643	0.7	-1.2, 2.7	0.460	0.7	-1.2, 2.7	0.457
24-47 weeks	110 (34%)	0.5	-1.4, 2.5	0.580	1.3	-0.7, 3.2	0.203	1.3	-0.7, 3.2	0.197
Still breastfeed at 48 weeks	73 (23%)	0.5	-1.5, 2.5	0.626	1.2	-0.8, 3.2	0.232	1.2	-0.8, 3.2	0.245
Gestational duration, completed weeks	329	0.1	-0.2, 0.4	0.352	0.3	-0.1, 0.6	0.112	0.3	-0.1, 0.6	0.095
Delivery mode
Vaginal delivery	274 (83%)	—	—		—	—		—	—
C-section	55 (17%)	0.2	-1.1, 1.4	0.780	-0.2	-1.5, 1.1	0.781	-0.1	-1.5, 1.2	0.834
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	235 (79%)	—	—		—	—		—	—
Between 6 and 12 months old	49 (16%)	-0.3	-1.7, 1.0	0.626	-0.9	-2.2, 0.4	0.171	-0.9	-2.3, 0.4	0.161
Not introduced at 12 months old	14 (4.7%)	1.4	-0.9, 3.7	0.237	1.4	-1.2, 4.1	0.291	1.4	-1.3, 4.1	0.305
Presence of pets
No	208 (72%)	—	—		—	—		—	—
One or more	82 (28%)	-0.8	-1.8, 0.3	0.159	-0.9	-2.0, 0.2	0.128	-0.9	-2.0, 0.2	0.119
Antibiotics use between 0-12 months old
No	224 (68%)	—	—		—	—		—	—
Yes	104 (32%)	0.2	-0.8, 1.2	0.728	0.4	-0.6, 1.5	0.418	0.4	-0.6, 1.5	0.426
Learning materials score at 3 years of age (HOME questionnaire)	300	-0.4	-0.8, -0.1	0.017
Language stimulation score at 3 years of age (HOME questionnaire)	300	0.1	-0.5, 0.7	0.704
Academic stimulation score at 3 years of age (HOME questionnaire)	300	0.1	-0.4, 0.7	0.596
Variety score at 3 years of age (HOME questionnaire)	300	-0.5	-0.9, -0.1	0.024
HOME questionnaire total score	300	-0.2	-0.4, 0.0	0.062	-0.1	-0.3, 0.1	0.211	-0.1	-0.3, 0.1	0.202
Maternal anxiety score during the third trimester of pregnancy	320	0.1	0.0, 0.3	0.110
Maternal depression score during the third trimester of pregnancy	319	0.1	-0.1, 0.3	0.244
Maternal anxiety and depression score during the third trimester of pregnancy	318	0.1	0.0, 0.2	0.102	0.1	0.0, 0.2	0.015	0.1	0.0, 0.2	0.019
Maternal anxiety score when child is one year old	258	0.1	-0.1, 0.2	0.390
Maternal depression score when child is one year old	258	0.1	-0.1, 0.3	0.354
Maternal anxiety and depression score when child is one year old	258	0.1	0.0, 0.2	0.279
Maternal active smoking during pregnancy
No	287 (94%)	—	—		—	—		—	—
Yes	18 (5.9%)	0.6	-1.4, 2.6	0.556	-0.3	-2.6, 2.1	0.806	-0.3	-2.6, 2.1	0.827
Maternal passive smoking during pregnancy
No	259 (82%)	—	—
Yes	55 (18%)	1.0	-0.2, 2.3	0.097
Child passive smoking during the first year of life
No	254 (77%)	—	—
Yes	75 (23%)	0.5	-0.6, 1.6	0.377
Child perinatal exposure to tabacco up to one year
No	207 (66%)	—	—
Yes	106 (34%)	1.1	0.1, 2.1	0.029
Child perinatal passive smoking up to one year
No	214 (68%)	—	—		—	—		—	—
Yes	103 (32%)	1.2	0.2, 2.1	0.024	0.9	-0.4, 2.1	0.177	0.9	-0.4, 2.2	0.166
Maternal alcohol consumption during pregnancy
Did not drink	100 (31%)	—	—
Drank only before finding out she was pregnant	157 (48%)	-0.3	-1.4, 0.8	0.604
Drank	70 (21%)	-0.2	-1.6, 1.1	0.738
Maternal alcohol consumption during pregnancy
Did not drink	100 (31%)	—	—
Drank only before finding out she was pregnant	157 (48%)	-0.3	-1.4, 0.8	0.604
<1drink/month when she knew she was pregnant	61 (19%)	-0.4	-1.8, 1.0	0.552
>1drink/month when she knew she was pregnant	9 (2.8%)	1.1	-1.9, 4.1	0.475
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	197 (63%)	—	—
Other	114 (37%)	-0.3	-1.3, 0.7	0.517
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	256 (82%)	—	—		—	—
Other	55 (18%)	-1.3	-2.6, 0.0	0.045	-0.8	-2.1, 0.6	0.263
Main mode of child care up to 1 year
Collective day care	263 (85%)	—	—					—	—
Other	48 (15%)	-1.0	-2.3, 0.4	0.152				-0.3	-1.8, 1.1	0.662
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	58 (19%)	—	—
Nursery assistant (out child home)	139 (45%)	0.4	-0.9, 1.8	0.528
Other	114 (37%)	0.0	-1.4, 1.4	0.968
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	96 (31%)	—	—
Nursery assistant (out child home)	160 (51%)	-0.2	-1.3, 0.9	0.726
Other	55 (18%)	-1.4	-2.9, 0.0	0.054
Main mode of child care up to 1 year
Collective day care	99 (32%)	—	—
Nursery assistant (out child home)	164 (53%)	-0.2	-1.3, 0.9	0.701
Other	48 (15%)	-1.1	-2.6, 0.4	0.147
Paternal education
≥5 years after graduation	151 (65%)	—	—
3-4 years after graduation	39 (17%)	0.9	-0.6, 2.5	0.246
2 years or less after graduation	42 (18%)	-0.2	-1.8, 1.3	0.752
Paternal age at child birth (years)	296	-0.1	-0.2, 0.0	0.289
Paternal age at child birth
23-31 years	96 (32%)	—	—
32-36 years	100 (34%)	-0.5	-1.8, 0.7	0.383
37-72 years	100 (34%)	-1.0	-2.2, 0.3	0.120
Child age at the SRS 3 years evaluation	329	0.1	0.0, 0.2	0.234
Child age at the SRS 3 years evaluation					0.1	0.0, 0.2	0.232	0.1	0.0, 0.2	0.236
No. Obs.					329			329
R²					0.124			0.121
Adjusted R²					0.052			0.048
1 N; n (%)
2 CI = Confidence Interval

Figure 70: Multivariate model hypothesis checking (outcome is BRIEF-P working memory score Y3, before inclusion of microbiota variables)

Plan/organization score Y3

Table 14:

Influence of maternal and child characteristics on the BRIEF-P plan and organization score at 2 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3351	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	335	0.1	-0.6, 0.7	0.866
Birth weight
<3 Kg	70 (21%)	—	—		—	—		—	—
3-3.4 Kg	165 (49%)	-0.2	-0.9, 0.6	0.678	-0.3	-1.2, 0.6	0.536	-0.3	-1.2, 0.6	0.518
≥3.5 Kg	100 (30%)	-0.1	-0.9, 0.8	0.893	-0.2	-1.4, 1.0	0.728	-0.2	-1.4, 1.0	0.711
Birth length (cm)	334	0.0	-0.1, 0.1	0.904
Birth length
<50 cm	121 (36%)	—	—		—	—		—	—
50-51 cm	135 (40%)	-0.1	-0.8, 0.6	0.745	-0.2	-1.1, 0.6	0.557	-0.2	-1.0, 0.6	0.564
≥52 cm	78 (23%)	0.2	-0.6, 1.0	0.567	0.2	-0.9, 1.3	0.767	0.2	-0.9, 1.3	0.749
Weight at one year (Kg)	331	0.0	-0.3, 0.3	0.875
Weight at one year
<8.5 Kg	58 (18%)	—	—
8.5-9.9 Kg	181 (55%)	0.5	-0.3, 1.4	0.201
≥10 Kg	92 (28%)	0.8	-0.2, 1.7	0.102
Length at one year (cm)	324	0.0	-0.1, 0.1	0.882
Length at one year
<75 cm	119 (37%)	—	—
75-77.9 cm	113 (35%)	-0.5	-1.2, 0.2	0.157
≥78 cm	92 (28%)	0.0	-0.8, 0.8	0.985
Weight at 3 years (Kg)	310	0.1	-0.1, 0.3	0.296
Weight at 3 years
9-13 Kg	105 (34%)	—	—
14 Kg	103 (33%)	0.3	-0.4, 1.1	0.418
15-20 Kg	102 (33%)	0.3	-0.5, 1.1	0.418
Length at 3 years (cm)	308	0.1	0.0, 0.1	0.219
Length at 3 years
81-93 cm	95 (31%)	—	—
94-95 cm	108 (35%)	-0.1	-0.8, 0.7	0.844
96-106 cm	105 (34%)	0.5	-0.3, 1.2	0.233
Child sex
Male	179 (53%)	—	—		—	—		—	—
Female	156 (47%)	-0.2	-0.8, 0.4	0.416	-0.2	-0.8, 0.5	0.558	-0.2	-0.8, 0.5	0.575
Maternal education
≥5 years after graduation	193 (58%)	—	—
3-4 years after graduation	89 (27%)	0.9	0.2, 1.6	0.008
2 years or less after graduation	51 (15%)	0.6	-0.3, 1.4	0.175
Maternal education
≥5 years after graduation	193 (58%)	—	—		—	—		—	—
<5 years after graduation	140 (42%)	0.8	0.2, 1.4	0.008	0.9	0.3, 1.6	0.003	0.9	0.3, 1.6	0.003
Maternal age at conception (years)	335	0.0	-0.1, 0.0	0.209	0.0	-0.1, 0.1	0.470	0.0	-0.1, 0.1	0.483
Maternal BMI before pregnancy (kg/m2)	334	0.0	-0.1, 0.1	0.833
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	212 (63%)	0.0	-0.9, 0.9	0.950	0.0	-0.9, 0.9	0.938	0.0	-0.9, 0.9	0.947
≥24 Kg/m2	76 (23%)	-0.2	-1.3, 0.8	0.663	-0.3	-1.3, 0.8	0.613	-0.3	-1.3, 0.8	0.601
Maternal parity
None	153 (46%)	—	—		—	—		—	—
1 child or more	182 (54%)	-0.5	-1.1, 0.1	0.086	-0.7	-1.3, 0.0	0.050	-0.7	-1.3, 0.0	0.052
Breastfeeding duration
Not breastfed	26 (8.0%)	—	—		—	—		—	—
<24 weeks	114 (35%)	-0.4	-1.6, 0.8	0.509	-0.2	-1.4, 1.0	0.719	-0.2	-1.4, 1.0	0.705
24-47 weeks	111 (34%)	0.2	-1.0, 1.3	0.797	0.6	-0.7, 1.9	0.369	0.6	-0.7, 1.9	0.376
Still breastfeed at 48 weeks	76 (23%)	-0.1	-1.4, 1.1	0.838	0.3	-1.0, 1.6	0.651	0.3	-1.0, 1.6	0.660
Gestational duration, completed weeks	335	0.0	-0.2, 0.2	0.841	0.1	-0.2, 0.3	0.603	0.1	-0.2, 0.3	0.598
Delivery mode
Vaginal delivery	281 (84%)	—	—		—	—		—	—
C-section	54 (16%)	0.1	-0.7, 1.0	0.733	-0.1	-1.0, 0.8	0.804	-0.1	-1.0, 0.8	0.810
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	241 (79%)	—	—		—	—		—	—
Between 6 and 12 months old	49 (16%)	0.0	-0.9, 0.9	0.977	-0.4	-1.3, 0.5	0.351	-0.4	-1.3, 0.5	0.349
Not introduced at 12 months old	15 (4.9%)	1.6	0.1, 3.0	0.037	1.6	0.1, 3.1	0.040	1.6	0.1, 3.1	0.038
Presence of pets
No	213 (72%)	—	—		—	—		—	—
One or more	84 (28%)	-0.3	-1.0, 0.4	0.368	-0.5	-1.2, 0.2	0.184	-0.5	-1.2, 0.2	0.187
Antibiotics use between 0-12 months old
No	232 (69%)	—	—		—	—		—	—
Yes	102 (31%)	0.1	-0.5, 0.8	0.727	0.2	-0.5, 0.8	0.614	0.2	-0.5, 0.8	0.622
Learning materials score at 3 years of age (HOME questionnaire)	306	0.0	-0.2, 0.3	0.689
Language stimulation score at 3 years of age (HOME questionnaire)	306	0.0	-0.4, 0.4	0.870
Academic stimulation score at 3 years of age (HOME questionnaire)	306	0.1	-0.2, 0.5	0.533
Variety score at 3 years of age (HOME questionnaire)	306	-0.1	-0.3, 0.2	0.692
HOME questionnaire total score	306	0.0	-0.1, 0.1	0.769	0.1	-0.1, 0.2	0.402	0.1	-0.1, 0.2	0.403
Maternal anxiety score during the third trimester of pregnancy	326	0.1	0.0, 0.2	0.108
Maternal depression score during the third trimester of pregnancy	325	0.1	0.0, 0.2	0.091
Maternal anxiety and depression score during the third trimester of pregnancy	324	0.1	0.0, 0.1	0.042	0.1	0.0, 0.2	0.013	0.1	0.0, 0.2	0.014
Maternal anxiety score when child is one year old	263	0.1	0.0, 0.2	0.107
Maternal depression score when child is one year old	263	0.1	-0.1, 0.2	0.373
Maternal anxiety and depression score when child is one year old	263	0.1	0.0, 0.1	0.123
Maternal active smoking during pregnancy
No	293 (94%)	—	—		—	—		—	—
Yes	19 (6.1%)	-0.1	-1.4, 1.2	0.922	-0.4	-1.8, 0.9	0.539	-0.4	-1.8, 0.9	0.541
Maternal passive smoking during pregnancy
No	264 (82%)	—	—
Yes	57 (18%)	-0.1	-0.9, 0.7	0.890
Child passive smoking during the first year of life
No	261 (78%)	—	—
Yes	74 (22%)	0.6	-0.1, 1.3	0.120
Child perinatal exposure to tabacco up to one year
No	214 (67%)	—	—
Yes	106 (33%)	0.4	-0.3, 1.0	0.251
Child perinatal passive smoking up to one year
No	221 (68%)	—	—		—	—		—	—
Yes	103 (32%)	0.5	-0.2, 1.1	0.159	0.4	-0.3, 1.2	0.255	0.4	-0.3, 1.2	0.245
Maternal alcohol consumption during pregnancy
Did not drink	101 (30%)	—	—
Drank only before finding out she was pregnant	161 (48%)	0.1	-0.6, 0.8	0.729
Drank	71 (21%)	0.3	-0.5, 1.2	0.460
Maternal alcohol consumption during pregnancy
Did not drink	101 (30%)	—	—
Drank only before finding out she was pregnant	161 (48%)	0.1	-0.6, 0.8	0.729
<1drink/month when she knew she was pregnant	60 (18%)	0.3	-0.6, 1.2	0.564
>1drink/month when she knew she was pregnant	11 (3.3%)	0.6	-1.1, 2.4	0.481
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	200 (63%)	—	—
Other	118 (37%)	-0.2	-0.9, 0.4	0.454
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	261 (82%)	—	—		—	—
Other	57 (18%)	-0.3	-1.1, 0.5	0.466	-0.2	-1.1, 0.6	0.592
Main mode of child care up to 1 year
Collective day care	268 (84%)	—	—					—	—
Other	50 (16%)	-0.3	-1.1, 0.5	0.484				-0.2	-1.1, 0.6	0.597
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	58 (18%)	—	—
Nursery assistant (out child home)	142 (45%)	0.6	-0.3, 1.4	0.196
Other	118 (37%)	0.2	-0.7, 1.0	0.726
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	98 (31%)	—	—
Nursery assistant (out child home)	163 (51%)	0.1	-0.6, 0.8	0.762
Other	57 (18%)	-0.2	-1.1, 0.7	0.621
Main mode of child care up to 1 year
Collective day care	101 (32%)	—	—
Nursery assistant (out child home)	167 (53%)	0.1	-0.6, 0.8	0.743
Other	50 (16%)	-0.2	-1.2, 0.7	0.635
Paternal education
≥5 years after graduation	150 (64%)	—	—
3-4 years after graduation	41 (17%)	0.1	-0.9, 1.1	0.823
2 years or less after graduation	45 (19%)	-0.3	-1.3, 0.6	0.490
Paternal age at child birth (years)	301	0.0	-0.1, 0.0	0.157
Paternal age at child birth
23-31 years	98 (33%)	—	—
32-36 years	101 (34%)	-0.6	-1.4, 0.1	0.098
37-72 years	102 (34%)	-0.9	-1.6, -0.1	0.027
Child age at the SRS 3 years evaluation	335	0.0	0.0, 0.1	0.208
Child age at the SRS 3 years evaluation					0.0	0.0, 0.1	0.311	0.0	0.0, 0.1	0.316
No. Obs.					335			335
R²					0.107			0.107
Adjusted R²					0.035			0.035
1 N; n (%)
2 CI = Confidence Interval

Figure 71: Multivariate model hypothesis checking (outcome is BRIEF-P plan and organization score Y3, before inclusion of microbiota variables)

IQ Y3

IQ verbal comprehension score Y3

Table 15:

Influence of maternal and child characteristics on the IQ verbal comprehension score at 3 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3151	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	315	-2.0	-4.8, 0.9	0.175
Birth weight
<3 Kg	63 (20%)	—	—		—	—		—	—
3-3.4 Kg	159 (50%)	-0.7	-4.1, 2.7	0.697	1.9	-2.1, 5.9	0.357	1.7	-2.3, 5.7	0.409
≥3.5 Kg	93 (30%)	-0.9	-4.7, 2.8	0.619	2.1	-3.1, 7.3	0.421	2.0	-3.2, 7.1	0.451
Birth length (cm)	314	-0.2	-0.8, 0.4	0.532
Birth length
<50 cm	116 (37%)	—	—		—	—		—	—
50-51 cm	124 (39%)	-2.0	-4.9, 1.0	0.191	-2.1	-5.6, 1.4	0.249	-2.0	-5.5, 1.5	0.264
≥52 cm	74 (24%)	-1.1	-4.5, 2.2	0.504	-0.4	-5.0, 4.2	0.868	-0.3	-4.9, 4.4	0.907
Weight at one year (Kg)	312	-0.6	-1.9, 0.6	0.316
Weight at one year
<8.5 Kg	56 (18%)	—	—
8.5-9.9 Kg	174 (56%)	-1.3	-4.7, 2.2	0.474
≥10 Kg	82 (26%)	-1.3	-5.2, 2.6	0.512
Length at one year (cm)	306	-0.4	-0.8, 0.1	0.109
Length at one year
<75 cm	116 (38%)	—	—
75-77.9 cm	109 (36%)	-3.4	-6.4, -0.4	0.025
≥78 cm	81 (26%)	-2.0	-5.2, 1.3	0.232
Weight at 3 years (Kg)	314	0.1	-0.7, 0.9	0.858
Weight at 3 years
9-13 Kg	104 (33%)	—	—
14 Kg	106 (34%)	-1.5	-4.6, 1.6	0.349
15-20 Kg	104 (33%)	-0.1	-3.2, 3.1	0.957
Length at 3 years (cm)	312	0.1	-0.3, 0.4	0.663
Length at 3 years
81-93 cm	95 (30%)	—	—
94-95 cm	109 (35%)	-0.5	-3.6, 2.7	0.774
96-106 cm	108 (35%)	1.1	-2.1, 4.2	0.500
Child sex
Male	167 (53%)	—	—		—	—		—	—
Female	148 (47%)	2.6	0.0, 5.1	0.046	1.5	-1.3, 4.2	0.293	1.5	-1.2, 4.3	0.279
Maternal education
≥5 years after graduation	182 (58%)	—	—
3-4 years after graduation	86 (27%)	-1.3	-4.3, 1.6	0.377
2 years or less after graduation	45 (14%)	-3.7	-7.5, 0.1	0.055
Maternal education
≥5 years after graduation	182 (58%)	—	—		—	—		—	—
<5 years after graduation	131 (42%)	-2.1	-4.7, 0.5	0.105	-1.5	-4.2, 1.1	0.255	-1.5	-4.2, 1.1	0.263
Maternal age at conception (years)	315	0.0	-0.4, 0.3	0.907	0.1	-0.3, 0.4	0.655	0.1	-0.3, 0.4	0.666
Maternal BMI before pregnancy (kg/m2)	314	0.0	-0.3, 0.4	0.939
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	198 (63%)	0.7	-3.0, 4.5	0.709	0.8	-3.0, 4.6	0.678	0.8	-3.0, 4.6	0.672
≥24 Kg/m2	71 (23%)	0.9	-3.4, 5.2	0.690	1.1	-3.3, 5.5	0.621	1.1	-3.4, 5.5	0.637
Maternal parity
None	139 (44%)	—	—		—	—		—	—
1 child or more	176 (56%)	-3.3	-5.8, -0.7	0.012	-3.0	-5.8, -0.2	0.036	-3.1	-5.9, -0.3	0.031
Breastfeeding duration
Not breastfed	25 (8.1%)	—	—		—	—		—	—
<24 weeks	102 (33%)	0.7	-4.3, 5.8	0.779	-0.7	-5.8, 4.5	0.802	-0.7	-5.9, 4.5	0.787
24-47 weeks	108 (35%)	2.4	-2.7, 7.4	0.353	1.0	-4.1, 6.1	0.692	1.0	-4.1, 6.1	0.701
Still breastfeed at 48 weeks	72 (23%)	4.3	-1.0, 9.5	0.112	4.3	-1.1, 9.6	0.117	4.2	-1.1, 9.5	0.123
Gestational duration, completed weeks	315	-0.3	-1.2, 0.5	0.451	-0.4	-1.4, 0.6	0.418	-0.4	-1.4, 0.6	0.445
Delivery mode
Vaginal delivery	263 (83%)	—	—		—	—		—	—
C-section	52 (17%)	-0.2	-3.7, 3.2	0.887	-1.2	-4.8, 2.4	0.507	-1.2	-4.7, 2.4	0.525
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	232 (80%)	—	—		—	—		—	—
Between 6 and 12 months old	45 (16%)	1.0	-2.7, 4.7	0.593	1.3	-2.7, 5.3	0.514	1.3	-2.7, 5.2	0.528
Not introduced at 12 months old	13 (4.5%)	-7.6	-14.0, -1.2	0.021	-6.0	-12.5, 0.5	0.069	-5.9	-12.4, 0.6	0.075
Presence of pets
No	203 (73%)	—	—		—	—		—	—
One or more	77 (28%)	0.3	-2.7, 3.3	0.850	0.5	-2.8, 3.7	0.779	0.5	-2.7, 3.7	0.765
Antibiotics use between 0-12 months old
No	212 (68%)	—	—		—	—		—	—
Yes	102 (32%)	-0.8	-3.6, 1.9	0.546	-0.7	-3.5, 2.1	0.631	-0.7	-3.5, 2.1	0.630
Learning materials score at 3 years of age (HOME questionnaire)	309	1.8	0.9, 2.8	<0.001
Language stimulation score at 3 years of age (HOME questionnaire)	309	1.1	-0.6, 2.7	0.199
Academic stimulation score at 3 years of age (HOME questionnaire)	309	1.9	0.5, 3.4	0.011
Variety score at 3 years of age (HOME questionnaire)	309	0.0	-1.2, 1.1	0.944
HOME questionnaire total score	309	0.8	0.3, 1.2	0.002	0.6	0.1, 1.1	0.021	0.6	0.1, 1.1	0.022
Maternal anxiety score during the third trimester of pregnancy	308	-0.3	-0.8, 0.1	0.161
Maternal depression score during the third trimester of pregnancy	307	-0.2	-0.7, 0.3	0.342
Maternal anxiety and depression score during the third trimester of pregnancy	306	-0.2	-0.5, 0.1	0.176	-0.1	-0.4, 0.2	0.335	-0.2	-0.5, 0.1	0.285
Maternal anxiety score when child is one year old	254	-0.4	-0.9, 0.0	0.078
Maternal depression score when child is one year old	254	-0.3	-0.8, 0.2	0.293
Maternal anxiety and depression score when child is one year old	254	-0.3	-0.6, 0.0	0.086
Maternal active smoking during pregnancy
No	272 (93%)	—	—		—	—		—	—
Yes	19 (6.5%)	-0.7	-6.1, 4.8	0.807	1.3	-4.9, 7.5	0.681	1.3	-4.9, 7.5	0.681
Maternal passive smoking during pregnancy
No	248 (82%)	—	—
Yes	54 (18%)	-1.5	-4.8, 1.9	0.389
Child passive smoking during the first year of life
No	240 (76%)	—	—
Yes	75 (24%)	-1.4	-4.4, 1.6	0.370
Child perinatal exposure to tabacco up to one year
No	198 (66%)	—	—
Yes	103 (34%)	-1.6	-4.4, 1.2	0.256
Child perinatal passive smoking up to one year
No	205 (67%)	—	—		—	—		—	—
Yes	100 (33%)	-1.2	-3.9, 1.6	0.407	-0.5	-3.5, 2.6	0.763	-0.4	-3.5, 2.7	0.792
Maternal alcohol consumption during pregnancy
Did not drink	95 (30%)	—	—
Drank only before finding out she was pregnant	151 (48%)	1.7	-1.3, 4.6	0.267
Drank	67 (21%)	-1.9	-5.5, 1.7	0.293
Maternal alcohol consumption during pregnancy
Did not drink	95 (30%)	—	—
Drank only before finding out she was pregnant	151 (48%)	1.7	-1.3, 4.6	0.266
<1drink/month when she knew she was pregnant	58 (19%)	-1.3	-5.1, 2.4	0.487
>1drink/month when she knew she was pregnant	9 (2.9%)	-5.8	-13.7, 2.1	0.149
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	183 (61%)	—	—
Other	116 (39%)	-1.3	-4.0, 1.3	0.328
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	246 (82%)	—	—		—	—
Other	53 (18%)	-3.0	-6.4, 0.4	0.081	-2.6	-6.3, 1.1	0.166
Main mode of child care up to 1 year
Collective day care	251 (84%)	—	—					—	—
Other	48 (16%)	-2.7	-6.2, 0.9	0.143				-2.1	-5.9, 1.6	0.269
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	53 (18%)	—	—
Nursery assistant (out child home)	130 (43%)	1.4	-2.3, 5.1	0.456
Other	116 (39%)	-0.3	-4.1, 3.4	0.858
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	94 (31%)	—	—
Nursery assistant (out child home)	152 (51%)	-0.8	-3.7, 2.2	0.609
Other	53 (18%)	-3.5	-7.4, 0.4	0.076
Main mode of child care up to 1 year
Collective day care	96 (32%)	—	—
Nursery assistant (out child home)	155 (52%)	-0.8	-3.8, 2.1	0.579
Other	48 (16%)	-3.2	-7.2, 0.8	0.120
Paternal education
≥5 years after graduation	142 (63%)	—	—
3-4 years after graduation	39 (17%)	1.0	-3.3, 5.2	0.652
2 years or less after graduation	43 (19%)	-2.3	-6.3, 1.8	0.277
Paternal age at child birth (years)	283	0.1	-0.2, 0.4	0.507
Paternal age at child birth
23-31 years	90 (32%)	—	—
32-36 years	94 (33%)	1.0	-2.4, 4.3	0.564
37-72 years	99 (35%)	-0.7	-4.0, 2.6	0.686
Child age at the IQ 3 years evaluation	315	0.3	0.0, 0.6	0.065
Child age at the IQ 3 years evaluation					0.3	0.0, 0.6	0.082	0.3	0.0, 0.6	0.082
No. Obs.					315			315
R²					0.124			0.121
Adjusted R²					0.048			0.045
1 N; n (%)
2 CI = Confidence Interval

Figure 72: Multivariate model hypothesis checking (outcome is IQ verbal comprehension score Y3, before inclusion of microbiota variables)

IQ visuospacial score Y3

Table 16:

Influence of maternal and child characteristics on the IQ visuospatial score at 3 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3151	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	315	0.7	-2.0, 3.4	0.618
Birth weight
<3 Kg	63 (20%)	—	—		—	—		—	—
3-3.4 Kg	159 (50%)	1.3	-2.0, 4.5	0.452	0.6	-3.4, 4.6	0.786	0.3	-3.7, 4.3	0.895
≥3.5 Kg	93 (30%)	0.9	-2.7, 4.5	0.611	0.0	-5.1, 5.1	0.990	-0.2	-5.3, 5.0	0.952
Birth length (cm)	314	0.2	-0.4, 0.8	0.503
Birth length
<50 cm	116 (37%)	—	—		—	—		—	—
50-51 cm	124 (39%)	0.9	-1.9, 3.8	0.511	0.4	-3.0, 3.9	0.808	0.5	-3.0, 4.0	0.776
≥52 cm	74 (24%)	0.3	-2.9, 3.6	0.839	0.3	-4.2, 4.9	0.883	0.5	-4.1, 5.1	0.836
Weight at one year (Kg)	312	0.0	-1.2, 1.3	0.947
Weight at one year
<8.5 Kg	56 (18%)	—	—
8.5-9.9 Kg	174 (56%)	0.3	-3.1, 3.7	0.870
≥10 Kg	82 (26%)	-0.2	-4.0, 3.6	0.921
Length at one year (cm)	306	0.0	-0.4, 0.4	0.975
Length at one year
<75 cm	116 (38%)	—	—
75-77.9 cm	109 (36%)	-1.9	-4.8, 1.0	0.206
≥78 cm	81 (26%)	-1.0	-4.2, 2.1	0.520
Weight at 3 years (Kg)	314	0.2	-0.6, 1.0	0.623
Weight at 3 years
9-13 Kg	104 (33%)	—	—
14 Kg	106 (34%)	-0.6	-3.7, 2.4	0.675
15-20 Kg	104 (33%)	-0.7	-3.7, 2.4	0.669
Length at 3 years (cm)	312	0.0	-0.4, 0.3	0.902
Length at 3 years
81-93 cm	95 (30%)	—	—
94-95 cm	109 (35%)	-1.0	-4.1, 2.1	0.532
96-106 cm	108 (35%)	0.2	-2.9, 3.3	0.913
Child sex
Male	167 (53%)	—	—		—	—		—	—
Female	148 (47%)	0.5	-2.0, 2.9	0.708	0.1	-2.6, 2.9	0.934	0.2	-2.6, 2.9	0.907
Maternal education
≥5 years after graduation	182 (58%)	—	—
3-4 years after graduation	86 (27%)	0.8	-2.0, 3.7	0.562
2 years or less after graduation	45 (14%)	0.2	-3.5, 3.8	0.926
Maternal education
≥5 years after graduation	182 (58%)	—	—		—	—		—	—
<5 years after graduation	131 (42%)	0.6	-1.9, 3.1	0.630	1.2	-1.4, 3.8	0.363	1.2	-1.4, 3.9	0.357
Maternal age at conception (years)	315	0.2	-0.2, 0.5	0.349	0.1	-0.3, 0.4	0.649	0.1	-0.3, 0.4	0.665
Maternal BMI before pregnancy (kg/m2)	314	-0.1	-0.4, 0.3	0.646
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	198 (63%)	0.9	-2.7, 4.5	0.622	0.5	-3.2, 4.3	0.772	0.6	-3.2, 4.3	0.764
≥24 Kg/m2	71 (23%)	1.7	-2.5, 5.9	0.429	1.6	-2.7, 6.0	0.464	1.6	-2.8, 5.9	0.483
Maternal parity
None	139 (44%)	—	—		—	—		—	—
1 child or more	176 (56%)	2.6	0.1, 5.0	0.041	2.4	-0.4, 5.2	0.089	2.3	-0.5, 5.1	0.104
Breastfeeding duration
Not breastfed	25 (8.1%)	—	—		—	—		—	—
<24 weeks	102 (33%)	3.6	-1.2, 8.4	0.138	3.3	-1.7, 8.3	0.200	3.2	-1.8, 8.2	0.210
24-47 weeks	108 (35%)	5.3	0.5, 10.0	0.030	5.1	0.0, 10.1	0.048	5.0	0.0, 10.1	0.050
Still breastfeed at 48 weeks	72 (23%)	6.1	1.1, 11.1	0.016	6.7	1.5, 11.9	0.011	6.7	1.4, 11.9	0.013
Gestational duration, completed weeks	315	0.0	-0.8, 0.8	0.948	0.0	-1.0, 1.0	0.982	0.0	-0.9, 1.0	0.928
Delivery mode
Vaginal delivery	263 (83%)	—	—		—	—		—	—
C-section	52 (17%)	-2.3	-5.6, 1.1	0.182	-2.4	-6.0, 1.1	0.176	-2.4	-5.9, 1.2	0.190
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	232 (80%)	—	—		—	—		—	—
Between 6 and 12 months old	45 (16%)	-0.8	-4.4, 2.9	0.672	-0.4	-3.8, 3.1	0.840	-0.4	-3.9, 3.1	0.814
Not introduced at 12 months old	13 (4.5%)	-3.0	-9.3, 3.4	0.357	-2.2	-8.8, 4.3	0.501	-2.1	-8.6, 4.4	0.525
Presence of pets
No	203 (73%)	—	—		—	—		—	—
One or more	77 (28%)	-1.4	-4.4, 1.5	0.339	-1.6	-4.7, 1.4	0.297	-1.6	-4.7, 1.5	0.312
Antibiotics use between 0-12 months old
No	212 (68%)	—	—		—	—		—	—
Yes	102 (32%)	1.6	-1.0, 4.2	0.225	1.7	-1.2, 4.5	0.248	1.7	-1.2, 4.5	0.250
Learning materials score at 3 years of age (HOME questionnaire)	309	0.7	-0.2, 1.6	0.117
Language stimulation score at 3 years of age (HOME questionnaire)	309	-0.2	-1.8, 1.4	0.799
Academic stimulation score at 3 years of age (HOME questionnaire)	309	0.0	-1.4, 1.4	0.989
Variety score at 3 years of age (HOME questionnaire)	309	0.5	-0.6, 1.7	0.358
HOME questionnaire total score	309	0.3	-0.2, 0.7	0.274	0.4	-0.2, 0.9	0.171	0.4	-0.2, 0.9	0.178
Maternal anxiety score during the third trimester of pregnancy	308	-0.4	-0.9, 0.0	0.048
Maternal depression score during the third trimester of pregnancy	307	0.3	-0.1, 0.8	0.167
Maternal anxiety and depression score during the third trimester of pregnancy	306	-0.1	-0.3, 0.2	0.707	0.0	-0.3, 0.3	0.853	-0.1	-0.4, 0.3	0.751
Maternal anxiety score when child is one year old	254	-0.4	-0.8, 0.1	0.127
Maternal depression score when child is one year old	254	0.5	0.0, 1.0	0.068
Maternal anxiety and depression score when child is one year old	254	0.0	-0.3, 0.3	0.917
Maternal active smoking during pregnancy
No	272 (93%)	—	—		—	—		—	—
Yes	19 (6.5%)	-2.0	-7.2, 3.2	0.453	-1.6	-7.0, 3.7	0.552	-1.6	-7.0, 3.7	0.551
Maternal passive smoking during pregnancy
No	248 (82%)	—	—
Yes	54 (18%)	-1.5	-4.8, 1.8	0.370
Child passive smoking during the first year of life
No	240 (76%)	—	—
Yes	75 (24%)	-1.2	-4.1, 1.7	0.431
Child perinatal exposure to tabacco up to one year
No	198 (66%)	—	—
Yes	103 (34%)	-1.5	-4.2, 1.2	0.270
Child perinatal passive smoking up to one year
No	205 (67%)	—	—		—	—		—	—
Yes	100 (33%)	-0.9	-3.6, 1.8	0.522	-0.6	-3.5, 2.3	0.678	-0.5	-3.4, 2.3	0.715
Maternal alcohol consumption during pregnancy
Did not drink	95 (30%)	—	—
Drank only before finding out she was pregnant	151 (48%)	-1.0	-3.9, 1.9	0.483
Drank	67 (21%)	-0.1	-3.6, 3.5	0.977
Maternal alcohol consumption during pregnancy
Did not drink	95 (30%)	—	—
Drank only before finding out she was pregnant	151 (48%)	-1.0	-3.9, 1.8	0.482
<1drink/month when she knew she was pregnant	58 (19%)	0.8	-2.9, 4.4	0.682
>1drink/month when she knew she was pregnant	9 (2.9%)	-5.3	-12.9, 2.4	0.175
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	183 (61%)	—	—
Other	116 (39%)	1.1	-1.6, 3.7	0.425
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	246 (82%)	—	—		—	—
Other	53 (18%)	-1.8	-5.2, 1.5	0.286	-3.4	-6.9, 0.1	0.058
Main mode of child care up to 1 year
Collective day care	251 (84%)	—	—					—	—
Other	48 (16%)	-1.4	-4.9, 2.1	0.447				-2.7	-6.3, 1.0	0.148
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	53 (18%)	—	—
Nursery assistant (out child home)	130 (43%)	-0.7	-4.3, 3.0	0.714
Other	116 (39%)	0.6	-3.1, 4.3	0.753
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	94 (31%)	—	—
Nursery assistant (out child home)	152 (51%)	-1.5	-4.4, 1.4	0.301
Other	53 (18%)	-2.8	-6.6, 1.0	0.153
Main mode of child care up to 1 year
Collective day care	96 (32%)	—	—
Nursery assistant (out child home)	155 (52%)	-1.8	-4.6, 1.1	0.233
Other	48 (16%)	-2.4	-6.4, 1.5	0.223
Paternal education
≥5 years after graduation	142 (63%)	—	—
3-4 years after graduation	39 (17%)	-1.5	-5.5, 2.5	0.454
2 years or less after graduation	43 (19%)	-2.7	-6.5, 1.1	0.166
Paternal age at child birth (years)	283	0.1	-0.1, 0.4	0.343
Paternal age at child birth
23-31 years	90 (32%)	—	—
32-36 years	94 (33%)	0.4	-2.7, 3.6	0.782
37-72 years	99 (35%)	0.9	-2.2, 4.0	0.576
Child age at the IQ 3 years evaluation	315	0.0	-0.3, 0.3	0.862
Child age at the IQ 3 years evaluation					0.0	-0.3, 0.3	0.939	0.0	-0.3, 0.3	0.940
No. Obs.					315			315
R²					0.078			0.073
Adjusted R²
1 N; n (%)
2 CI = Confidence Interval

Figure 73: Multivariate model hypothesis checking (outcome is IQ visuospacial score Y3, before inclusion of microbiota variables)

IQ work memory score Y3

Table 17:

Influence of maternal and child characteristics on the IQ work memory score at 3 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3151	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	315	-1.6	-4.3, 1.2	0.258
Birth weight
<3 Kg	63 (20%)	—	—		—	—		—	—
3-3.4 Kg	159 (50%)	0.8	-2.4, 4.1	0.610	0.3	-3.6, 4.3	0.875	0.1	-3.9, 4.0	0.974
≥3.5 Kg	93 (30%)	-1.4	-4.9, 2.1	0.441	-2.2	-7.2, 2.8	0.390	-2.4	-7.4, 2.7	0.354
Birth length (cm)	314	-0.1	-0.6, 0.5	0.785
Birth length
<50 cm	116 (37%)	—	—		—	—		—	—
50-51 cm	124 (39%)	0.0	-2.9, 2.8	0.973	0.3	-3.1, 3.7	0.846	0.4	-3.0, 3.8	0.822
≥52 cm	74 (24%)	-1.3	-4.6, 1.9	0.415	0.0	-4.5, 4.5	0.998	0.1	-4.4, 4.6	0.959
Weight at one year (Kg)	312	-1.6	-2.8, -0.4	0.008
Weight at one year
<8.5 Kg	56 (18%)	—	—
8.5-9.9 Kg	174 (56%)	-2.6	-5.9, 0.7	0.116
≥10 Kg	82 (26%)	-5.0	-8.7, -1.3	0.009
Length at one year (cm)	306	-0.4	-0.8, 0.0	0.080
Length at one year
<75 cm	116 (38%)	—	—
75-77.9 cm	109 (36%)	-2.8	-5.7, 0.1	0.055
≥78 cm	81 (26%)	-2.8	-5.9, 0.3	0.078
Weight at 3 years (Kg)	314	-0.9	-1.6, -0.1	0.025
Weight at 3 years
9-13 Kg	104 (33%)	—	—
14 Kg	106 (34%)	-0.9	-3.9, 2.1	0.563
15-20 Kg	104 (33%)	-2.5	-5.5, 0.5	0.098
Length at 3 years (cm)	312	-0.3	-0.6, 0.1	0.109
Length at 3 years
81-93 cm	95 (30%)	—	—
94-95 cm	109 (35%)	-2.7	-5.7, 0.4	0.084
96-106 cm	108 (35%)	-2.0	-5.1, 1.0	0.193
Child sex
Male	167 (53%)	—	—		—	—		—	—
Female	148 (47%)	1.7	-0.7, 4.2	0.169	1.3	-1.4, 4.0	0.353	1.3	-1.4, 4.0	0.341
Maternal education
≥5 years after graduation	182 (58%)	—	—
3-4 years after graduation	86 (27%)	0.5	-2.4, 3.3	0.746
2 years or less after graduation	45 (14%)	-0.8	-4.4, 2.8	0.674
Maternal education
≥5 years after graduation	182 (58%)	—	—		—	—		—	—
<5 years after graduation	131 (42%)	0.0	-2.5, 2.5	0.974	0.2	-2.4, 2.8	0.886	0.2	-2.4, 2.8	0.884
Maternal age at conception (years)	315	-0.1	-0.5, 0.2	0.362	-0.2	-0.6, 0.1	0.239	-0.2	-0.6, 0.1	0.231
Maternal BMI before pregnancy (kg/m2)	314	0.0	-0.4, 0.3	0.870
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	198 (63%)	-2.1	-5.7, 1.4	0.240	-3.0	-6.7, 0.7	0.111	-2.9	-6.6, 0.7	0.117
≥24 Kg/m2	71 (23%)	-1.1	-5.2, 3.0	0.597	-1.6	-5.8, 2.7	0.477	-1.6	-5.9, 2.7	0.464
Maternal parity
None	139 (44%)	—	—		—	—		—	—
1 child or more	176 (56%)	1.7	-0.7, 4.2	0.167	2.9	0.2, 5.7	0.036	2.8	0.1, 5.6	0.044
Breastfeeding duration
Not breastfed	25 (8.1%)	—	—		—	—		—	—
<24 weeks	102 (33%)	0.7	-4.1, 5.5	0.779	0.8	-4.3, 5.8	0.767	0.7	-4.3, 5.7	0.782
24-47 weeks	108 (35%)	0.1	-4.7, 4.9	0.970	-0.6	-5.6, 4.3	0.804	-0.7	-5.6, 4.3	0.796
Still breastfeed at 48 weeks	72 (23%)	4.0	-1.0, 9.0	0.117	4.2	-1.0, 9.3	0.112	4.1	-1.1, 9.2	0.120
Gestational duration, completed weeks	315	0.0	-0.8, 0.8	0.970	0.2	-0.8, 1.1	0.731	0.2	-0.8, 1.2	0.681
Delivery mode
Vaginal delivery	263 (83%)	—	—		—	—		—	—
C-section	52 (17%)	-1.3	-4.6, 2.0	0.447	-0.5	-3.9, 3.0	0.795	-0.4	-3.9, 3.1	0.828
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	232 (80%)	—	—		—	—		—	—
Between 6 and 12 months old	45 (16%)	-1.7	-5.2, 1.8	0.349	-0.5	-4.0, 3.0	0.775	-0.6	-4.1, 3.0	0.754
Not introduced at 12 months old	13 (4.5%)	-4.2	-10.3, 1.9	0.176	-3.7	-10.3, 2.9	0.269	-3.6	-10.3, 3.0	0.281
Presence of pets
No	203 (73%)	—	—		—	—		—	—
One or more	77 (28%)	-0.8	-3.7, 2.1	0.600	-0.7	-3.8, 2.3	0.636	-0.7	-3.8, 2.4	0.643
Antibiotics use between 0-12 months old
No	212 (68%)	—	—		—	—		—	—
Yes	102 (32%)	0.9	-1.7, 3.5	0.506	1.0	-1.8, 3.8	0.469	1.0	-1.8, 3.8	0.467
Learning materials score at 3 years of age (HOME questionnaire)	309	0.3	-0.7, 1.2	0.580
Language stimulation score at 3 years of age (HOME questionnaire)	309	1.4	-0.1, 3.0	0.071
Academic stimulation score at 3 years of age (HOME questionnaire)	309	0.8	-0.6, 2.2	0.248
Variety score at 3 years of age (HOME questionnaire)	309	-0.3	-1.4, 0.8	0.591
HOME questionnaire total score	309	0.2	-0.2, 0.7	0.328	0.3	-0.2, 0.8	0.220	0.3	-0.2, 0.8	0.228
Maternal anxiety score during the third trimester of pregnancy	308	-0.3	-0.7, 0.1	0.158
Maternal depression score during the third trimester of pregnancy	307	-0.1	-0.6, 0.3	0.619
Maternal anxiety and depression score during the third trimester of pregnancy	306	-0.1	-0.4, 0.1	0.279	-0.1	-0.4, 0.2	0.360	-0.1	-0.4, 0.1	0.303
Maternal anxiety score when child is one year old	254	-0.1	-0.5, 0.4	0.782
Maternal depression score when child is one year old	254	0.0	-0.5, 0.5	0.977
Maternal anxiety and depression score when child is one year old	254	0.0	-0.3, 0.3	0.850
Maternal active smoking during pregnancy
No	272 (93%)	—	—		—	—		—	—
Yes	19 (6.5%)	-4.8	-9.9, 0.3	0.062	-3.8	-9.3, 1.6	0.166	-3.9	-9.3, 1.6	0.166
Maternal passive smoking during pregnancy
No	248 (82%)	—	—
Yes	54 (18%)	-1.3	-4.6, 1.9	0.430
Child passive smoking during the first year of life
No	240 (76%)	—	—
Yes	75 (24%)	-2.2	-5.0, 0.7	0.139
Child perinatal exposure to tabacco up to one year
No	198 (66%)	—	—
Yes	103 (34%)	-1.5	-4.1, 1.1	0.254
Child perinatal passive smoking up to one year
No	205 (67%)	—	—		—	—		—	—
Yes	100 (33%)	-1.0	-3.6, 1.7	0.468	0.2	-2.7, 3.1	0.910	0.2	-2.7, 3.1	0.881
Maternal alcohol consumption during pregnancy
Did not drink	95 (30%)	—	—
Drank only before finding out she was pregnant	151 (48%)	-0.4	-3.2, 2.5	0.800
Drank	67 (21%)	-0.9	-4.4, 2.6	0.613
Maternal alcohol consumption during pregnancy
Did not drink	95 (30%)	—	—
Drank only before finding out she was pregnant	151 (48%)	-0.4	-3.2, 2.5	0.800
<1drink/month when she knew she was pregnant	58 (19%)	-0.5	-4.2, 3.1	0.769
>1drink/month when she knew she was pregnant	9 (2.9%)	-3.1	-10.7, 4.5	0.416
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	183 (61%)	—	—
Other	116 (39%)	-0.6	-3.2, 1.9	0.634
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	246 (82%)	—	—		—	—
Other	53 (18%)	-1.6	-4.9, 1.6	0.326	-2.8	-6.3, 0.7	0.117
Main mode of child care up to 1 year
Collective day care	251 (84%)	—	—					—	—
Other	48 (16%)	-1.0	-4.4, 2.4	0.563				-2.0	-5.8, 1.8	0.294
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	53 (18%)	—	—
Nursery assistant (out child home)	130 (43%)	-1.0	-4.5, 2.5	0.581
Other	116 (39%)	-1.3	-4.9, 2.3	0.468
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	94 (31%)	—	—
Nursery assistant (out child home)	152 (51%)	-1.3	-4.1, 1.6	0.383
Other	53 (18%)	-2.4	-6.1, 1.3	0.202
Main mode of child care up to 1 year
Collective day care	96 (32%)	—	—
Nursery assistant (out child home)	155 (52%)	-1.4	-4.2, 1.4	0.314
Other	48 (16%)	-1.9	-5.7, 1.9	0.331
Paternal education
≥5 years after graduation	142 (63%)	—	—
3-4 years after graduation	39 (17%)	-0.8	-4.7, 3.1	0.678
2 years or less after graduation	43 (19%)	1.0	-2.7, 4.7	0.599
Paternal age at child birth (years)	283	0.1	-0.2, 0.3	0.532
Paternal age at child birth
23-31 years	90 (32%)	—	—
32-36 years	94 (33%)	1.2	-1.9, 4.4	0.439
37-72 years	99 (35%)	0.7	-2.4, 3.9	0.641
Child age at the IQ 3 years evaluation	315	0.1	-0.2, 0.4	0.493
Child age at the IQ 3 years evaluation					0.1	-0.2, 0.4	0.665	0.1	-0.2, 0.4	0.663
No. Obs.					315			315
R²					0.088			0.085
Adjusted R²					0.008
1 N; n (%)
2 CI = Confidence Interval

Figure 74: Multivariate model hypothesis checking (outcome is IQ work memory score Y3, before inclusion of microbiota variables)

IQ total score Y3

Table 18:

Influence of maternal and child characteristics on the IQ total score at 3 years (uni and multivariate models).

Characteristic		Univariate models			Multivariate model test 1			Multivariate model test 2
	N = 3151	Beta	95% CI2	p-value	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight (Kg)	315	-1.0	-3.8, 1.8	0.490
Birth weight
<3 Kg	63 (20%)	—	—		—	—		—	—
3-3.4 Kg	159 (50%)	0.5	-2.8, 3.8	0.781	1.2	-2.8, 5.2	0.552	0.9	-3.1, 4.9	0.675
≥3.5 Kg	93 (30%)	-0.3	-4.0, 3.3	0.854	0.3	-4.8, 5.5	0.896	0.1	-5.0, 5.2	0.970
Birth length (cm)	314	0.0	-0.6, 0.6	0.968
Birth length
<50 cm	116 (37%)	—	—		—	—		—	—
50-51 cm	124 (39%)	-0.3	-3.1, 2.6	0.858	-0.2	-3.7, 3.2	0.888	-0.2	-3.6, 3.3	0.928
≥52 cm	74 (24%)	-0.6	-3.9, 2.7	0.731	0.4	-4.2, 5.0	0.861	0.6	-4.1, 5.2	0.803
Weight at one year (Kg)	312	-0.8	-2.1, 0.4	0.188
Weight at one year
<8.5 Kg	56 (18%)	—	—
8.5-9.9 Kg	174 (56%)	-1.6	-5.0, 1.8	0.358
≥10 Kg	82 (26%)	-2.6	-6.5, 1.2	0.182
Length at one year (cm)	306	-0.3	-0.8, 0.1	0.141
Length at one year
<75 cm	116 (38%)	—	—
75-77.9 cm	109 (36%)	-3.6	-6.6, -0.7	0.016
≥78 cm	81 (26%)	-2.6	-5.8, 0.6	0.107
Weight at 3 years (Kg)	314	-0.1	-0.9, 0.6	0.716
Weight at 3 years
9-13 Kg	104 (33%)	—	—
14 Kg	106 (34%)	-1.6	-4.6, 1.5	0.320
15-20 Kg	104 (33%)	-1.1	-4.2, 2.0	0.485
Length at 3 years (cm)	312	-0.1	-0.4, 0.3	0.729
Length at 3 years
81-93 cm	95 (30%)	—	—
94-95 cm	109 (35%)	-1.6	-4.7, 1.6	0.324
96-106 cm	108 (35%)	-0.1	-3.2, 3.1	0.963
Child sex
Male	167 (53%)	—	—		—	—		—	—
Female	148 (47%)	2.1	-0.4, 4.6	0.099	1.4	-1.4, 4.1	0.319	1.5	-1.3, 4.2	0.301
Maternal education
≥5 years after graduation	182 (58%)	—	—
3-4 years after graduation	86 (27%)	0.7	-2.2, 3.6	0.643
2 years or less after graduation	45 (14%)	-1.5	-5.3, 2.2	0.412
Maternal education
≥5 years after graduation	182 (58%)	—	—		—	—		—	—
<5 years after graduation	131 (42%)	-0.1	-2.6, 2.5	0.951	0.7	-2.0, 3.3	0.606	0.7	-1.9, 3.4	0.600
Maternal age at conception (years)	315	0.0	-0.3, 0.4	0.805	0.0	-0.3, 0.4	0.829	0.0	-0.3, 0.4	0.852
Maternal BMI before pregnancy (kg/m2)	314	0.0	-0.4, 0.3	0.828
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—		—	—
19-23.9 Kg/m2	198 (63%)	0.5	-3.1, 4.2	0.779	0.0	-3.7, 3.8	0.991	0.1	-3.7, 3.8	0.975
≥24 Kg/m2	71 (23%)	1.3	-3.0, 5.5	0.560	1.0	-3.3, 5.4	0.643	0.9	-3.4, 5.3	0.670
Maternal parity
None	139 (44%)	—	—		—	—		—	—
1 child or more	176 (56%)	0.3	-2.2, 2.8	0.799	0.8	-2.0, 3.6	0.583	0.6	-2.2, 3.4	0.657
Breastfeeding duration
Not breastfed	25 (8.1%)	—	—		—	—		—	—
<24 weeks	102 (33%)	2.3	-2.6, 7.3	0.358	1.6	-3.4, 6.7	0.526	1.6	-3.5, 6.7	0.545
24-47 weeks	108 (35%)	3.8	-1.1, 8.7	0.129	3.0	-2.0, 8.1	0.235	3.0	-2.0, 8.0	0.243
Still breastfeed at 48 weeks	72 (23%)	5.9	0.7, 11.0	0.026	6.3	1.1, 11.6	0.018	6.2	1.0, 11.5	0.021
Gestational duration, completed weeks	315	-0.2	-1.0, 0.7	0.703	-0.2	-1.2, 0.8	0.661	-0.2	-1.2, 0.8	0.730
Delivery mode
Vaginal delivery	263 (83%)	—	—		—	—		—	—
C-section	52 (17%)	-1.6	-5.0, 1.7	0.343	-1.8	-5.3, 1.7	0.316	-1.7	-5.3, 1.9	0.345
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	232 (80%)	—	—		—	—		—	—
Between 6 and 12 months old	45 (16%)	-0.4	-4.0, 3.2	0.845	0.3	-3.3, 4.0	0.861	0.3	-3.4, 4.0	0.893
Not introduced at 12 months old	13 (4.5%)	-6.9	-13.2, -0.6	0.031	-5.4	-12.2, 1.4	0.120	-5.2	-12.1, 1.6	0.130
Presence of pets
No	203 (73%)	—	—		—	—		—	—
One or more	77 (28%)	-0.9	-3.8, 2.1	0.566	-0.8	-4.0, 2.3	0.597	-0.8	-4.0, 2.4	0.614
Antibiotics use between 0-12 months old
No	212 (68%)	—	—		—	—		—	—
Yes	102 (32%)	0.5	-2.1, 3.2	0.691	0.7	-2.1, 3.5	0.637	0.7	-2.1, 3.5	0.638
Learning materials score at 3 years of age (HOME questionnaire)	309	1.5	0.5, 2.4	0.002
Language stimulation score at 3 years of age (HOME questionnaire)	309	0.8	-0.8, 2.3	0.337
Academic stimulation score at 3 years of age (HOME questionnaire)	309	1.3	-0.1, 2.7	0.077
Variety score at 3 years of age (HOME questionnaire)	309	0.3	-0.9, 1.4	0.650
HOME questionnaire total score	309	0.6	0.2, 1.1	0.009	0.6	0.1, 1.1	0.017	0.6	0.1, 1.1	0.019
Maternal anxiety score during the third trimester of pregnancy	308	-0.5	-1.0, -0.1	0.015
Maternal depression score during the third trimester of pregnancy	307	0.1	-0.4, 0.5	0.828
Maternal anxiety and depression score during the third trimester of pregnancy	306	-0.2	-0.5, 0.1	0.187	-0.1	-0.5, 0.2	0.364	-0.2	-0.5, 0.1	0.280
Maternal anxiety score when child is one year old	254	-0.4	-0.9, 0.0	0.076
Maternal depression score when child is one year old	254	0.1	-0.4, 0.6	0.607
Maternal anxiety and depression score when child is one year old	254	-0.1	-0.4, 0.2	0.419
Maternal active smoking during pregnancy
No	272 (93%)	—	—		—	—		—	—
Yes	19 (6.5%)	-3.0	-8.3, 2.2	0.257	-1.8	-7.2, 3.6	0.522	-1.8	-7.2, 3.6	0.522
Maternal passive smoking during pregnancy
No	248 (82%)	—	—
Yes	54 (18%)	-2.1	-5.4, 1.2	0.220
Child passive smoking during the first year of life
No	240 (76%)	—	—
Yes	75 (24%)	-2.0	-5.0, 0.9	0.175
Child perinatal exposure to tabacco up to one year
No	198 (66%)	—	—
Yes	103 (34%)	-1.9	-4.6, 0.8	0.158
Child perinatal passive smoking up to one year
No	205 (67%)	—	—		—	—		—	—
Yes	100 (33%)	-1.3	-4.0, 1.5	0.362	-0.5	-3.4, 2.4	0.731	-0.4	-3.3, 2.5	0.774
Maternal alcohol consumption during pregnancy
Did not drink	95 (30%)	—	—
Drank only before finding out she was pregnant	151 (48%)	0.6	-2.3, 3.5	0.697
Drank	67 (21%)	-0.8	-4.4, 2.7	0.641
Maternal alcohol consumption during pregnancy
Did not drink	95 (30%)	—	—
Drank only before finding out she was pregnant	151 (48%)	0.6	-2.3, 3.5	0.696
<1drink/month when she knew she was pregnant	58 (19%)	0.2	-3.5, 3.9	0.933
>1drink/month when she knew she was pregnant	9 (2.9%)	-7.3	-15.1, 0.4	0.064
Main mode of child care at 6 months (2 categories, optimized 2)
Collective day care	183 (61%)	—	—
Other	116 (39%)	-0.1	-2.7, 2.6	0.954
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	246 (82%)	—	—		—	—
Other	53 (18%)	-3.1	-6.5, 0.2	0.068	-4.2	-7.8, -0.7	0.020
Main mode of child care up to 1 year
Collective day care	251 (84%)	—	—					—	—
Other	48 (16%)	-2.5	-6.0, 1.0	0.165				-3.2	-6.9, 0.5	0.086
Main mode of child care at 6 months (3 categories, optimized 2)
Collective day care	53 (18%)	—	—
Nursery assistant (out child home)	130 (43%)	0.3	-3.3, 3.9	0.878
Other	116 (39%)	0.1	-3.6, 3.8	0.947
Main mode of child care at 12 months (3 categories, optimized 2)
Collective day care	94 (31%)	—	—
Nursery assistant (out child home)	152 (51%)	-1.5	-4.4, 1.4	0.300
Other	53 (18%)	-4.1	-7.9, -0.3	0.036
Main mode of child care up to 1 year
Collective day care	96 (32%)	—	—
Nursery assistant (out child home)	155 (52%)	-1.7	-4.6, 1.1	0.236
Other	48 (16%)	-3.5	-7.5, 0.4	0.076
Paternal education
≥5 years after graduation	142 (63%)	—	—
3-4 years after graduation	39 (17%)	-0.3	-4.4, 3.8	0.883
2 years or less after graduation	43 (19%)	-2.6	-6.5, 1.4	0.202
Paternal age at child birth (years)	283	0.1	-0.2, 0.3	0.509
Paternal age at child birth
23-31 years	90 (32%)	—	—
32-36 years	94 (33%)	1.2	-2.0, 4.3	0.475
37-72 years	99 (35%)	0.0	-3.2, 3.1	0.995
Child age at the IQ 3 years evaluation	315	0.1	-0.1, 0.4	0.323
Child age at the IQ 3 years evaluation					0.1	-0.2, 0.4	0.499	0.1	-0.2, 0.4	0.499
No. Obs.					315			315
R²					0.099			0.091
Adjusted R²					0.020			0.011
1 N; n (%)
2 CI = Confidence Interval

Figure 75: Multivariate model hypothesis checking (outcome is IQ total score Y3, before inclusion of microbiota variables)

Part 3: Main analysis

Final covariates

Justification du choix des covariables inclues dans le modèle et leur codage :

• Age de l’enfant lors du test de neurodeveloppement :

  • Distribution : ok (Table 6, Figure 37, Figure 38, Figure 39)

  • Données manquantes : CBCL (20/356 (5.6%)), IQ (41/356 (12%)), SRS et BRIEF-P (15/356 (4.2%)) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) : non statistiquement associé avec les outcomes neurodeveloppement sauf un tendance (p<0.1) pour l’IQ verbal comprenhension Table 15)

    --> Choix final : les variables sont inclues, selon l’outcome, en continue

• Poids et taille de l’enfant à la naissance, à un an ou 3 ans :

  • Distribution : ok (Table 6, Figure 57, Figure 58, Figure 59, Figure 60, Figure 61, Figure 62)

  • Corrélations : les variables sont corrélées (Figure 36)

  • Données manquantes : le poids et la taille à la naissance sont les variables avec le moins de données manquantes (<2% VS autour de 15-20% pour les autres, Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • Les relations ne semblent pas linéaires entre le poids et la taille à la naissance et le neurodéveloppement de l’enfant (Table 7 à Table 18)

  • Elimination du poids et de la taille à 1, 2 et 3 ans pour respecter la chronologie (le microbiote a été prélevé à un an)

    --> Choix final: on choisit les variables poids et taille à la naissance, en catégoriel (3 catégories, po_w_kg_3cat et po_he_3cat)

• Age des parents :

  • Distribution : ok (Table 6, Figure 40, Figure 41)

  • Corrélations : les variables âge de la mère à la conception et âge du père à la naissance sont corrélées (Figure 36)

  • Données manquantes : l’âge de la mère n’a aucune donnée manquante contrairement à l’âge du père (17% de NA, Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • l’âge du père et de la mère sont associés au comportement de l’enfant mais pas au qi les deux variables semblent avoir une relation linéaire les deux variables sont associées dans le même sens

    --> Choix final : on choisit la variable âge de la mère, en continu (mo_age)

• Niveau d’éducation des parents:

  • Distribution : ok, catégories équilibrées (Table 5)

  • Données manquantes : il y a moins de données manquantes sur la variables mère (0.4% VS 39%, Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • le niveau d’éducation de la mère est associée à SRS totale et Plan/organization score at 3 years (BRIEF-P) à trois ans

  • Choix des catégories : Ariane et Vicente ont utilisé 2 catégories (≥5 years after graduation VS <5 years after graduation)

    --> Choix final : on choisit la variable éducation de la mère en 2 catégories (mo_dipl_2cat)

• IMC de la mère avant la grossesse :

  • Distribution : beaucoup d’outliers (Table 6, Figure 42)

  • Données manquantes : 1/356 (0.3%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • L’IMC de la mère avant la grossesse n’est pas statistiquement associée aux outcomes de neurodeveloppement

    • La relation ne semble pas linéaire

Choix final : on choisit la variable IMC de la mère avant la grossesse en 3 catégories (mo_bmi_bepr_3cat)

• Sexe de l’enfant :

  • Distribution (Male/Female): ok, catégories équilibrées (Table 5)

  • Données manquantes : 0/356 (0%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • Le sexe de l’enfant n’est pas associé aux outcomes de neurodeveloppement

    • Sauf en univarié pour BRIEF-P inhibit score (Beta : -1.2; CI95%:-2.3, 0.0; p=0.042, female compared to male, Table 10)

    • Sauf en univarié pour IQ verbal comprehension score Y3 (Beta : 2.6; CI95% : 0.0, 5.1; p=0.046, female, compared to male, Table 15)

Choix final : on inclut la variable sexe de l’enfant (ch_sex)

• Parité :

  • Distribution (None/1 child or more) : ok, catégories équilibrées (Table 5)

  • Données manquantes : 0/356 (0%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • Statistiquement associé avec presque tous les outcomes de neurodeveloppement

    • Le fait d’avoir déjà eu un enfant ou plus est associé à une diminution des outcomes BRIEF-P, SRS, CBCL et une augmentation du QI

    • Sauf IQ verbal comprehension score Y3 : sens de l’association innatendu

Choix final : on inclut la variable parité (mo_par_2cat)

• Durée de l’allaitement :

  • Distribution : ok, pas d’outliers (Figure 49, Table 6)

  • Données manquantes : 9/356 (2.5%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • La relation entre la durée de l’allaitement et les outcomes de neuroveloppement semble linéaire

Choix final : on inclut la variable catégorielle car pour le microbiote il y a une grosse différenc eattendu entre les enfants allaités des enfants non allaités (ch_bf_duration_till48w_4cat)

• Durée de la gestation :

  • Distribution : ok (Figure 50, Table 6)

  • Données manquantes : 0/356 (0%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • La durée de la gestation n’est pas statistiquement associée aux outcomes de neurodeveloppement (car les enfants sont presque tous nés à terme)

Choix final : on inclut la variable en continue (po_gd)

• Mode d’accouchement :

  • Distribution (Vaginal delivery / C-section) : ok (Table 5)

  • Données manquantes : 0/356 (0%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • Le mode d’accouchement n’est pas statistiquement associé aux outcomes de neurodeveloppement

Choix final : on inclut la variable en continue (po_delmod)

• Période d’introduction de la nourriture solide :

  • Distribution (Between 0 and 6 months old / Between 6 and 12 months old / Not introduced at 12 months old) : ok (Table 5)

  • Données manquantes : 37/356 (10%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18)

Choix final : on inclut la variable en catégoriel (ch_food_intro_Y1_3cat)

• Présence d’animaux de compagnie :

  • Distribution (No / One or more) : ok (Table 5)

  • Données manquantes : 45/356 (13%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • non statistiquement associé

Choix final : on inclut la variable en catégoriel (mo_pets)

• Prescription d’antibiotiques entre la naissance et l’âge de 1 an :

  • Distribution (No / Yes) : ok (Table 5)

    • Données manquantes : 1/356 (0.3%) (Table 5)

    • Régressions uni et multivariées (Table 7 à Table 18) :

      • non statistiquement associé

Choix final : on inclut la variable en catégoriel (ch_antibio_Y1_2cat)

• Questionnaires HOME à 3 ans :

  • Corrélations : les variables HOME sont corrélées entre elles (Figure 36) –> on choisit la plus générale (home_total_y3)

  • Distribution : continue, ok (Table 6, Figure 52, Figure 53, Figure 54, Figure 56)

  • Données manquantes : 43/356 (12%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • HOME questionnaire total score était associé à CBCL externe score Y2, SRS total score Y3, IQ verbal comprehension score Y3, IQ total score Y3

Choix final : on inclut la variable en continue (home_total_y3)

• Score d’anxiété et de dépression de la mère, au 3ème trimestre et lorsque l’enfant a l’âge de 1 ans :

  • Corrélations : les variables sont corrélées entre elles (Figure 36) –> on choisit la plus générale et la plus loin chronologiquement des variables d’expositions et d’outcomes –> le score totale d’anxiété et de dépression de la mère au T3

  • Distribution : continue, ok (Table 6, Figure 43, Figure 44, Figure 45, Figure 46, Figure 47, Figure 48) - Données manquantes : 14/356 (3.9%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • La variable score d’anxiété et de dépression de la mère à T3 est statistiquement associée aux outcomes de neurodeveloppmement (CBCL Y2, SRS Y3, BRIEF-P Y3) mais pas au QI

Choix final : on inclut la variable score totale d’anxiété et de dépression de la mère au T3 (mo_hadtotscore_grt3_imp)

• Consomation d’alcool pendant la grossesse :

  • la variable est peu précise, peu de femme ont réélement bu pendant la grossesse (Table 5, Table 6)

Choix final : nous n’incluons pas cette variable dans les modèles

• Tabagisme périnatale :

  • 3 variables initiales sont disponibles :

    • Tabagisme passif de la mère pendant la grossesse (oui/non)

    • Tabagisme actif de la mère pendant la grossesse (oui/non)

    • Tabagisme passif de l’enfant de la naissance à un an (oui/non)

  • Distribution (No / Yes) : ok (Table 5)

  • Données manquantes : ok (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • non statistiquement associé ou tendance (en univarié)

Choix final : on regroupe en 2 variables catégorielles oui / non

une variable tabagisme périnatale passif (tabagisme passif de la mère pendant la grossesse + tabagisme passif de l’enfant de la naissance à un an (ch_tabacco_passive_up_to_Y1)

une variable tabagisme actif de la mère pendant la grossesse (mo_tob_gr_anyt_yn_n2)

• Mode de garde principal de l’enfant à 6 et 12 mois :

  • 2 variables sont disponibles : mode de garde à 6 mois (Collective day care/other), mode de garde à 12 mois (Collective day care/other)

  • on teste 2 models :

    • un premier où l’on inclut la variable main child care at 12 months (ch_care_main_12m_opt2_2c, Multivariate model test 1)

    • un deuxième où l’on inclut une variable main child care up to 12 months (ch_care_main_6m_12m_opt2_2c, Multivariate model test 2) : ici tous les enfants qui ont un mode de garde principal collectif à 6 ou 12 mois sont dans la catégorie collective day care

  • Distribution : ok, il n’y a pas une grande différence entre les deux variables (Table 5)

  • Données manquantes : 25/356 (7.0%) (Table 5)

  • Régressions uni et multivariées (Table 7 à Table 18) :

    • La variable main mode of child care at 12 months est associée à une augmentation de BRIEF-P shift score Y3 et à une diminition de IQ total scoreY3 (Collective day care est la catégorie de référence) dans les modèles uni et multivariés

    • La variable main mode of child care up to 12 months tendait à être associée à une augmentation de BRIEF-P shift score Y3 et à une diminition de IQ total scoreY3 (Collective day care est la catégorie de référence) dans les modèles uni et multivariés

Choix final : on inclut la variable en catégoriel (ch_care_main_12m_opt2_2c)

Table 19:

Description final covariates

Characteristic	Included, N = 3561	Excluded, N = 1281	p-value2
Birth weight			0.96
<3 Kg	74 (21%)	25 (20%)
3-3.4 Kg	174 (49%)	62 (50%)
≥3.5 Kg	108 (30%)	36 (29%)
Birth length			0.44
<50 cm	130 (37%)	40 (34%)
50-51 cm	141 (40%)	54 (46%)
≥52 cm	84 (24%)	23 (20%)
Maternal education			0.80
≥5 years after graduation	201 (57%)	71 (55%)
<5 years after graduation	153 (43%)	57 (45%)
Maternal age at conception (years)	32 (30, 35)	32 (30, 35)	0.29
Maternal BMI before pregnancy			0.40
<19 Kg/m2	48 (14%)	12 (10%)
19-23.9 Kg/m2	223 (63%)	78 (62%)
≥24 Kg/m2	84 (24%)	35 (28%)
Child sex			0.96
Male	190 (53%)	66 (54%)
Female	166 (47%)	57 (46%)
Maternal parity			0.88
None	164 (46%)	58 (45%)
1 child or more	192 (54%)	70 (55%)
Breastfeeding duration			0.54
Not breastfed	29 (8%)	11 (12%)
<24 weeks	122 (35%)	35 (37%)
24-47 weeks	117 (34%)	32 (34%)
Still breastfeed at 48 weeks	79 (23%)	16 (17%)
Gestational duration, completed weeks	40 (39, 40)	39 (38, 40)	0.31
Delivery mode			0.54
Vaginal delivery	298 (84%)	100 (81%)
C-section	58 (16%)	23 (19%)
Period of introduction of solid food 0-12 months old			0.09
Between 0 and 6 months old	253 (79%)	40 (67%)
Between 6 and 12 months old	50 (16%)	16 (27%)
Not introduced at 12 months old	16 (5%)	4 (7%)
Presence of pets			0.30
No	222 (71%)	49 (65%)
One or more	89 (29%)	26 (35%)
Antibiotics use between 0-12 months old			0.02
No	246 (69%)	86 (81%)
Yes	109 (31%)	20 (19%)
HOME questionnaire total score	25 (23, 26)	25 (23, 27)	0.68
Maternal anxiety and depression score during the third trimester of pregnancy	10 (7, 13)	11 (7, 15)	0.16
Maternal active smoking during pregnancy			0.30
No	310 (94%)	91 (91%)
Yes	20 (6%)	9 (9%)
Child perinatal passive smoking up to one year			0.08
No	232 (67%)	45 (57%)
Yes	112 (33%)	34 (43%)
Main mode of child care at 12 months			0.28
Collective day care	271 (82%)	55 (76%)
Other	60 (18%)	17 (24%)
1 n (%); Median (IQR)
2 Pearson’s Chi-squared test; Wilcoxon rank sum test; Fisher’s exact test

Final sample sizes

Figure 76: Flow chart of the participants

A rediscuter si on prend un seul effectif commun ?

CBCL scores Y2

Interne score Y2

Table 20:

Adjusted associations between gut microbiota parameters and the CBCL interne score.

Characteristic	Child CBCL interne score at 2 years
	N	Beta	95% CI1	p-value
Specific richness	332	0.01	-0.01, 0.03	0.536
Shannon diversity	332	0.38	-0.56, 1.33	0.424
Phylum Firmicutes	336	0.00	-0.03, 0.02	0.842
Phylum Actinobacteria	336	0.02	-0.01, 0.04	0.151
Phylum Bacteroidetes	336	0.00	-0.03, 0.03	0.869
Phylum Proteobacteria	336	-0.03	-0.06, 0.00	0.080
Genus Bifidobacterium	336	0.02	-0.01, 0.04	0.134
Genus Bacteroides	336	-0.02	-0.05, 0.02	0.323
Genus Blautia	336	-0.04	-0.09, 0.01	0.131
Genera Escherichia and Shigella	336	-0.02	-0.06, 0.01	0.210
1 CI = Confidence Interval

Externe score Y2

Table 21:

Adjusted associations between gut microbiota parameters and the CBCL externe score at 2 years.

Characteristic	Child CBCL externe score at 2 years
	N	Beta	95% CI1	p-value
Specific richness	331	-0.01	-0.03, 0.02	0.629
Shannon diversity	331	0.50	-0.76, 1.75	0.436
Phylum Firmicutes	335	0.02	-0.01, 0.06	0.156
Phylum Actinobacteria	335	0.02	-0.01, 0.05	0.232
Phylum Bacteroidetes	335	-0.01	-0.05, 0.03	0.547
Phylum Proteobacteria	335	-0.05	-0.10, -0.01	0.024
Genus Bifidobacterium	335	0.02	-0.01, 0.05	0.203
Genus Bacteroides	335	-0.02	-0.06, 0.02	0.396
Genus Blautia	335	0.03	-0.04, 0.10	0.377
Genera Escherichia and Shigella	335	-0.04	-0.09, 0.01	0.158
1 CI = Confidence Interval

SRS total score Y3

Table 22:

Adjusted associations between gut microbiota parameters and the SRS total score at 3 years.

Characteristic	Child SRS total score at 3 years
	N	Beta	95% CI1	p-value
Specific richness	327	0.02	-0.04, 0.07	0.570
Shannon diversity	327	-0.10	-2.58, 2.38	0.938
Phylum Firmicutes	332	-0.01	-0.08, 0.06	0.768
Phylum Actinobacteria	332	0.04	-0.02, 0.10	0.202
Phylum Bacteroidetes	332	0.02	-0.06, 0.10	0.647
Phylum Proteobacteria	332	-0.10	-0.19, -0.02	0.018
Genus Bifidobacterium	332	0.04	-0.02, 0.11	0.165
Genus Bacteroides	332	0.02	-0.06, 0.10	0.601
Genus Blautia	332	-0.05	-0.19, 0.09	0.511
Genera Escherichia and Shigella	332	-0.10	-0.20, -0.01	0.038
1 CI = Confidence Interval

BRIEF-P Y3

Inhibition score Y3

Table 23:

Adjusted associations between gut microbiota parameters and the BRIEF-P inhibition score at 3 years.

Characteristic	Child inhibition score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness	325	0.00	-0.02, 0.03	0.711
Shannon diversity	325	0.07	-0.97, 1.11	0.894
Phylum Firmicutes	330	0.01	-0.01, 0.04	0.317
Phylum Actinobacteria	330	0.02	0.00, 0.05	0.099
Phylum Bacteroidetes	330	-0.02	-0.05, 0.02	0.358
Phylum Proteobacteria	330	-0.04	-0.07, 0.00	0.031
Genus Bifidobacterium	330	0.02	0.00, 0.05	0.103
Genus Bacteroides	330	-0.01	-0.05, 0.02	0.486
Genus Blautia	330	0.02	-0.04, 0.08	0.551
Genera Escherichia and Shigella	330	-0.02	-0.06, 0.02	0.291
1 CI = Confidence Interval

Shift score Y3

Table 24:

Adjusted associations between gut microbiota parameters and the BRIEF-P shift score at 3 years.

Characteristic	Child shift score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness	333	0.00	-0.01, 0.01	0.766
Shannon diversity	333	-0.16	-0.75, 0.42	0.587
Phylum Firmicutes	338	0.00	-0.02, 0.02	0.992
Phylum Actinobacteria	338	0.01	-0.01, 0.02	0.352
Phylum Bacteroidetes	338	0.00	-0.02, 0.02	0.912
Phylum Proteobacteria	338	-0.02	-0.04, 0.00	0.126
Genus Bifidobacterium	338	0.01	-0.01, 0.02	0.280
Genus Bacteroides	338	0.00	-0.02, 0.02	0.653
Genus Blautia	338	-0.01	-0.05, 0.02	0.465
Genera Escherichia and Shigella	338	-0.01	-0.04, 0.01	0.238
1 CI = Confidence Interval

Emotional control score Y3

Table 25:

Adjusted associations between gut microbiota parameters and the BRIEF-P emotional control score at 3 years.

Characteristic	Child emotional control score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness	332	0.01	0.00, 0.03	0.090
Shannon diversity	332	0.53	-0.16, 1.22	0.130
Phylum Firmicutes	337	0.01	-0.01, 0.03	0.500
Phylum Actinobacteria	337	0.00	-0.01, 0.02	0.735
Phylum Bacteroidetes	337	0.01	-0.01, 0.03	0.283
Phylum Proteobacteria	337	-0.03	-0.05, -0.01	0.017
Genus Bifidobacterium	337	0.00	-0.01, 0.02	0.715
Genus Bacteroides	337	0.02	-0.01, 0.04	0.185
Genus Blautia	337	0.00	-0.04, 0.04	0.888
Genera Escherichia and Shigella	337	-0.03	-0.06, 0.00	0.028
1 CI = Confidence Interval

Working memory score Y3

Table 26:

Adjusted associations between gut microbiota parameters and the BRIEF-P working memory score at 3 years.

Characteristic	Child working memory score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness	324	0.01	-0.01, 0.03	0.430
Shannon diversity	324	0.05	-0.83, 0.92	0.915
Phylum Firmicutes	329	0.01	-0.01, 0.03	0.429
Phylum Actinobacteria	329	0.02	-0.01, 0.04	0.131
Phylum Bacteroidetes	329	-0.03	-0.06, 0.00	0.032
Phylum Proteobacteria	329	-0.02	-0.05, 0.01	0.125
Genus Bifidobacterium	329	0.02	0.00, 0.04	0.123
Genus Bacteroides	329	-0.03	-0.06, 0.00	0.031
Genus Blautia	329	-0.02	-0.07, 0.03	0.457
Genera Escherichia and Shigella	329	-0.03	-0.06, 0.01	0.126
1 CI = Confidence Interval

Plan/organization score Y3

Table 27:

Adjusted associations between gut microbiota parameters and the BRIEF-P plan and organization score at 3 years.

Characteristic	Child plan/organization score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness	330	0.01	0.00, 0.02	0.149
Shannon diversity	330	0.19	-0.37, 0.74	0.508
Phylum Firmicutes	335	0.02	0.00, 0.03	0.026
Phylum Actinobacteria	335	0.01	-0.01, 0.02	0.417
Phylum Bacteroidetes	335	-0.02	-0.03, 0.00	0.045
Phylum Proteobacteria	335	-0.02	-0.03, 0.00	0.113
Genus Bifidobacterium	335	0.01	-0.01, 0.02	0.383
Genus Bacteroides	335	-0.02	-0.04, 0.00	0.032
Genus Blautia	335	0.00	-0.03, 0.03	>0.999
Genera Escherichia and Shigella	335	-0.01	-0.03, 0.01	0.246
1 CI = Confidence Interval

IQ Y3

Verbal comprehension score Y3

Table 28:

Adjusted associations between gut microbiota parameters and the IQ verbal comprehension score at 3 years.

Characteristic	Child verbal comprehension score at 3 years (IQ test)
	N	Beta	95% CI1	p-value
Specific richness	310	-0.01	-0.06, 0.04	0.690
Shannon diversity	310	-1.28	-3.66, 1.10	0.290
Phylum Firmicutes	315	-0.02	-0.09, 0.04	0.535
Phylum Actinobacteria	315	-0.02	-0.08, 0.03	0.423
Phylum Bacteroidetes	315	0.03	-0.05, 0.10	0.473
Phylum Proteobacteria	315	0.00	-0.09, 0.08	0.960
Genus Bifidobacterium	315	-0.02	-0.08, 0.04	0.462
Genus Bacteroides	315	0.03	-0.04, 0.11	0.400
Genus Blautia	315	0.06	-0.08, 0.19	0.394
Genera Escherichia and Shigella	315	-0.05	-0.14, 0.05	0.361
1 CI = Confidence Interval

Visuospatiale score Y3

Table 29:

Adjusted associations between gut microbiota parameters and the IQ visuospatiale score at 3 years.

Characteristic	Child visuospatiale score at 3 years (IQ test)
	N	Beta	95% CI1	p-value
Specific richness	310	0.00	-0.05, 0.05	0.922
Shannon diversity	310	0.35	-1.99, 2.69	0.768
Phylum Firmicutes	315	-0.01	-0.07, 0.06	0.781
Phylum Actinobacteria	315	0.00	-0.06, 0.06	0.908
Phylum Bacteroidetes	315	0.04	-0.03, 0.11	0.243
Phylum Proteobacteria	315	-0.03	-0.11, 0.05	0.500
Genus Bifidobacterium	315	0.00	-0.06, 0.06	0.911
Genus Bacteroides	315	0.05	-0.02, 0.13	0.174
Genus Blautia	315	0.00	-0.13, 0.13	0.985
Genera Escherichia and Shigella	315	-0.04	-0.14, 0.06	0.411
1 CI = Confidence Interval

Work memory score Y3

Table 30:

Adjusted associations between gut microbiota parameters and the IQ work memory score at 3 years.

Characteristic	Child work memory score at 3 years (IQ test)
	N	Beta	95% CI1	p-value
Specific richness	310	-0.01	-0.05, 0.04	0.800
Shannon diversity	310	-1.04	-3.34, 1.25	0.372
Phylum Firmicutes	315	-0.01	-0.07, 0.06	0.819
Phylum Actinobacteria	315	0.03	-0.02, 0.09	0.261
Phylum Bacteroidetes	315	-0.02	-0.09, 0.06	0.669
Phylum Proteobacteria	315	-0.04	-0.12, 0.04	0.347
Genus Bifidobacterium	315	0.03	-0.03, 0.09	0.317
Genus Bacteroides	315	-0.01	-0.08, 0.07	0.814
Genus Blautia	315	0.00	-0.13, 0.13	0.956
Genera Escherichia and Shigella	315	-0.06	-0.16, 0.04	0.216
1 CI = Confidence Interval

Total IQ score Y3

Table 31:

Adjusted associations between gut microbiota parameters and the IQ total score at 3 years.

Characteristic	Child total IQ score at 3 years
	N	Beta	95% CI1	p-value
Specific richness	310	0.00	-0.05, 0.05	0.997
Shannon diversity	310	-0.64	-3.00, 1.71	0.590
Phylum Firmicutes	315	-0.02	-0.09, 0.04	0.452
Phylum Actinobacteria	315	0.00	-0.06, 0.05	0.898
Phylum Bacteroidetes	315	0.04	-0.03, 0.11	0.310
Phylum Proteobacteria	315	-0.02	-0.11, 0.06	0.610
Genus Bifidobacterium	315	0.00	-0.06, 0.05	0.886
Genus Bacteroides	315	0.05	-0.03, 0.12	0.205
Genus Blautia	315	0.03	-0.10, 0.16	0.687
Genera Escherichia and Shigella	315	-0.06	-0.15, 0.04	0.249
1 CI = Confidence Interval

Part 4: Additional analysis

Covariates effects on the outcomes

CBCL Y2

Interne score Y2

Characteristic		Univariate models			Multivariate model
	N = 3361	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	70 (21%)	—	—		—	—
3-3.4 Kg	166 (49%)	0.8	-0.6, 2.1	0.265	1.0	-0.6, 2.6	0.215
≥3.5 Kg	100 (30%)	0.9	-0.6, 2.3	0.246	1.5	-0.5, 3.5	0.149
Birth length
<50 cm	123 (37%)	—	—		—	—
50-51 cm	135 (40%)	0.2	-1.0, 1.3	0.783	-0.3	-1.7, 1.1	0.701
≥52 cm	77 (23%)	0.0	-1.4, 1.4	0.995	-0.6	-2.4, 1.3	0.560
Maternal education
≥5 years after graduation	191 (57%)	—	—		—	—
<5 years after graduation	143 (43%)	0.1	-0.9, 1.2	0.777	-0.2	-1.2, 0.9	0.762
Maternal age at conception (years)	336	-0.1	-0.3, 0.0	0.049	-0.1	-0.3, 0.0	0.147
Maternal BMI before pregnancy
<19 Kg/m2	47 (14%)	—	—		—	—
19-23.9 Kg/m2	209 (62%)	0.1	-1.4, 1.7	0.856	0.4	-1.1, 1.9	0.622
≥24 Kg/m2	79 (24%)	0.6	-1.1, 2.3	0.489	0.5	-1.2, 2.3	0.572
Child sex
Male	181 (54%)	—	—		—	—
Female	155 (46%)	0.2	-0.9, 1.2	0.739	0.6	-0.5, 1.7	0.295
Maternal parity
None	157 (47%)	—	—		—	—
1 child or more	179 (53%)	-1.2	-2.2, -0.2	0.022	-1.5	-2.7, -0.4	0.009
Breastfeeding duration
Not breastfed	28 (8.5%)	—	—		—	—
<24 weeks	114 (35%)	-0.2	-2.2, 1.8	0.833	-0.1	-2.1, 1.9	0.952
24-47 weeks	113 (34%)	-0.3	-2.3, 1.7	0.803	0.1	-1.9, 2.2	0.887
Still breastfeed at 48 weeks	73 (22%)	0.8	-1.3, 2.9	0.434	0.9	-1.1, 3.0	0.375
Gestational duration, completed weeks	336	0.2	-0.1, 0.5	0.229	0.1	-0.3, 0.5	0.648
Delivery mode
Vaginal delivery	282 (84%)	—	—		—	—
C-section	54 (16%)	-0.2	-1.6, 1.2	0.805	-0.4	-1.9, 1.1	0.595
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	247 (80%)	—	—		—	—
Between 6 and 12 months old	47 (15%)	-0.1	-1.6, 1.5	0.946	-0.7	-2.3, 0.9	0.365
Not introduced at 12 months old	13 (4.2%)	-0.7	-3.4, 2.0	0.588	0.5	-2.4, 3.3	0.746
Presence of pets
No	214 (72%)	—	—		—	—
One or more	83 (28%)	0.3	-0.9, 1.5	0.589	0.3	-1.0, 1.6	0.648
Antibiotics use between 0-12 months old
No	230 (69%)	—	—		—	—
Yes	105 (31%)	-0.7	-1.8, 0.4	0.220	-0.6	-1.8, 0.5	0.279
HOME questionnaire total score	302	-0.2	-0.4, 0.0	0.050	-0.2	-0.4, 0.0	0.096
Maternal anxiety and depression score during the third trimester of pregnancy	327	0.2	0.1, 0.3	<0.001	0.2	0.1, 0.4	<0.001
Maternal active smoking during pregnancy	18 (5.8%)
No		—	—		—	—
Yes		-0.1	-2.3, 2.1	0.926	-0.2	-2.8, 2.4	0.888
Child perinatal passive smoking up to one year	109 (33%)
No		—	—		—	—
Yes		1.2	0.1, 2.3	0.040	0.9	-0.3, 2.0	0.127
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	260 (82%)	—	—		—	—
Other	57 (18%)	-0.4	-1.8, 0.9	0.531	-0.5	-2.0, 0.9	0.473
Child age at the CBCL 2 years evaluation	336	0.1	-0.1, 0.3	0.292
Child age at the CBCL 2 years evaluation					0.1	-0.1, 0.3	0.365
No. Obs.					336
R²					0.125
Adjusted R²					0.054
1 n (%); N
2 CI = Confidence Interval

Externe score Y2

Characteristic		Univariate models			Multivariate model
	N = 3351	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	70 (21%)	—	—		—	—
3-3.4 Kg	166 (50%)	0.0	-1.7, 1.8	0.981	-0.5	-2.7, 1.6	0.611
≥3.5 Kg	99 (30%)	0.5	-1.5, 2.4	0.630	-0.1	-2.8, 2.6	0.940
Birth length
<50 cm	123 (37%)	—	—		—	—
50-51 cm	134 (40%)	0.2	-1.3, 1.7	0.801	-0.3	-2.1, 1.6	0.789
≥52 cm	77 (23%)	0.6	-1.2, 2.4	0.545	0.1	-2.4, 2.6	0.917
Maternal education
≥5 years after graduation	191 (57%)	—	—		—	—
<5 years after graduation	142 (43%)	1.2	-0.1, 2.6	0.078	0.7	-0.7, 2.1	0.304
Maternal age at conception (years)	335	-0.2	-0.3, 0.0	0.065	-0.2	-0.4, 0.0	0.053
Maternal BMI before pregnancy
<19 Kg/m2	47 (14%)	—	—		—	—
19-23.9 Kg/m2	209 (63%)	0.9	-1.1, 2.9	0.387	0.9	-1.1, 3.0	0.383
≥24 Kg/m2	78 (23%)	0.9	-1.4, 3.2	0.432	0.7	-1.6, 3.1	0.547
Child sex
Male	180 (54%)	—	—		—	—
Female	155 (46%)	-0.9	-2.2, 0.5	0.217	-0.3	-1.8, 1.2	0.702
Maternal parity
None	157 (47%)	—	—		—	—
1 child or more	178 (53%)	-0.1	-1.4, 1.3	0.930	-0.2	-1.7, 1.3	0.811
Breastfeeding duration
Not breastfed	28 (8.6%)	—	—		—	—
<24 weeks	113 (35%)	-0.5	-3.1, 2.2	0.727	-0.1	-2.8, 2.6	0.941
24-47 weeks	113 (35%)	-0.8	-3.4, 1.8	0.556	0.1	-2.6, 2.8	0.942
Still breastfeed at 48 weeks	73 (22%)	0.0	-2.8, 2.7	0.974	0.4	-2.4, 3.2	0.777
Gestational duration, completed weeks	335	0.1	-0.3, 0.6	0.557	0.1	-0.4, 0.6	0.663
Delivery mode
Vaginal delivery	281 (84%)	—	—		—	—
C-section	54 (16%)	0.1	-1.8, 1.9	0.939	-0.1	-2.1, 1.9	0.934
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	247 (80%)	—	—		—	—
Between 6 and 12 months old	47 (15%)	-0.4	-2.4, 1.6	0.701	-0.8	-2.8, 1.3	0.469
Not introduced at 12 months old	13 (4.2%)	0.6	-2.9, 4.2	0.718	0.8	-3.0, 4.6	0.672
Presence of pets
No	214 (72%)	—	—		—	—
One or more	83 (28%)	-0.9	-2.5, 0.7	0.273	-1.1	-2.7, 0.5	0.183
Antibiotics use between 0-12 months old
No	229 (69%)	—	—		—	—
Yes	105 (31%)	0.3	-1.2, 1.8	0.694	0.4	-1.1, 1.9	0.629
HOME questionnaire total score	301	-0.4	-0.6, -0.1	0.010	-0.3	-0.6, 0.0	0.044
Maternal anxiety and depression score during the third trimester of pregnancy	326	0.2	0.1, 0.3	0.005	0.2	0.1, 0.4	0.004
Maternal active smoking during pregnancy	18 (5.8%)
No		—	—		—	—
Yes		2.8	-0.3, 5.8	0.072	1.6	-1.4, 4.6	0.282
Child perinatal passive smoking up to one year	109 (33%)
No		—	—		—	—
Yes		1.6	0.2, 3.1	0.026	1.0	-0.5, 2.5	0.187
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	260 (82%)	—	—		—	—
Other	57 (18%)	-0.6	-2.4, 1.2	0.525	-0.6	-2.5, 1.3	0.555
Child age at the CBCL 2 years evaluation	335	0.0	-0.3, 0.2	0.795
Child age at the CBCL 2 years evaluation					0.0	-0.3, 0.2	0.878
No. Obs.					335
R²					0.092
Adjusted R²					0.018
1 n (%); N
2 CI = Confidence Interval

SRS total score 3Y

Characteristic		Univariate models			Multivariate model
	N = 3321	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	69 (21%)	—	—		—	—
3-3.4 Kg	163 (49%)	1.2	-2.5, 4.8	0.523	1.6	-2.6, 5.7	0.462
≥3.5 Kg	100 (30%)	2.3	-1.7, 6.3	0.254	3.0	-2.3, 8.3	0.271
Birth length
<50 cm	121 (37%)	—	—		—	—
50-51 cm	132 (40%)	-0.3	-3.5, 2.9	0.854	-1.1	-4.8, 2.5	0.534
≥52 cm	78 (24%)	1.1	-2.6, 4.8	0.557	-1.1	-6.0, 3.8	0.650
Maternal education
≥5 years after graduation	191 (58%)	—	—		—	—
<5 years after graduation	139 (42%)	3.7	0.8, 6.5	0.011	4.0	1.2, 6.8	0.005
Maternal age at conception (years)	332	-0.3	-0.7, 0.1	0.105	-0.1	-0.5, 0.3	0.708
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—
19-23.9 Kg/m2	208 (63%)	1.2	-2.9, 5.4	0.561	2.0	-2.0, 6.0	0.325
≥24 Kg/m2	77 (23%)	1.3	-3.5, 6.0	0.599	1.7	-3.0, 6.3	0.474
Child sex
Male	177 (53%)	—	—		—	—
Female	155 (47%)	-0.3	-3.1, 2.5	0.817	0.4	-2.4, 3.3	0.762
Maternal parity
None	151 (45%)	—	—		—	—
1 child or more	181 (55%)	-4.7	-7.5, -2.0	<0.001	-6.5	-9.5, -3.6	<0.001
Breastfeeding duration
Not breastfed	25 (7.7%)	—	—		—	—
<24 weeks	113 (35%)	-3.2	-8.9, 2.4	0.263	-2.0	-7.4, 3.5	0.474
24-47 weeks	112 (35%)	-3.9	-9.5, 1.8	0.182	-1.5	-7.0, 3.9	0.582
Still breastfeed at 48 weeks	74 (23%)	-4.4	-10.4, 1.5	0.143	-2.8	-8.5, 2.9	0.335
Gestational duration, completed weeks	332	0.6	-0.3, 1.5	0.188	0.4	-0.6, 1.4	0.388
Delivery mode
Vaginal delivery	278 (84%)	—	—		—	—
C-section	54 (16%)	1.1	-2.7, 4.8	0.583	-0.4	-4.2, 3.5	0.842
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	238 (79%)	—	—		—	—
Between 6 and 12 months old	49 (16%)	0.6	-3.4, 4.5	0.784	-1.7	-5.8, 2.4	0.403
Not introduced at 12 months old	15 (5.0%)	6.0	-0.8, 12.7	0.083	6.6	-0.3, 13.5	0.059
Presence of pets
No	211 (72%)	—	—		—	—
One or more	83 (28%)	0.1	-3.2, 3.4	0.944	-0.3	-3.9, 3.3	0.865
Antibiotics use between 0-12 months old
No	228 (69%)	—	—		—	—
Yes	103 (31%)	-0.2	-3.2, 2.8	0.894	0.0	-3.0, 3.0	0.989
HOME questionnaire total score	303	-0.8	-1.3, -0.3	0.004	-0.7	-1.2, -0.1	0.018
Maternal anxiety and depression score during the third trimester of pregnancy	321	0.5	0.2, 0.8	<0.001	0.6	0.3, 1.0	<0.001
Maternal active smoking during pregnancy	19 (6.1%)
No		—	—		—	—
Yes		-1.0	-6.9, 4.9	0.737	-0.7	-7.0, 5.6	0.832
Child perinatal passive smoking up to one year	103 (32%)
No		—	—		—	—
Yes		-0.7	-3.7, 2.3	0.653	-1.7	-5.0, 1.5	0.300
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	257 (82%)	—	—		—	—
Other	58 (18%)	-1.4	-5.1, 2.3	0.456	-0.9	-4.8, 2.9	0.625
Child age at the SRS 3 years evaluation	332	0.3	0.0, 0.6	0.081
Child age at the SRS 3 years evaluation					0.2	-0.1, 0.5	0.280
No. Obs.					332
R²					0.171
Adjusted R²					0.104
1 n (%); N
2 CI = Confidence Interval

BRIEF-P Y3

Inhibit score Y3

Characteristic		Univariate models			Multivariate model
	N = 3301	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	68 (21%)	—	—		—	—
3-3.4 Kg	161 (49%)	0.1	-1.4, 1.5	0.931	-0.5	-2.2, 1.3	0.607
≥3.5 Kg	101 (31%)	0.0	-1.6, 1.6	0.993	-1.2	-3.4, 1.0	0.297
Birth length
<50 cm	118 (36%)	—	—		—	—
50-51 cm	131 (40%)	0.8	-0.5, 2.1	0.230	1.1	-0.5, 2.6	0.171
≥52 cm	80 (24%)	1.3	-0.1, 2.8	0.074	2.0	0.0, 4.0	0.055
Maternal education
≥5 years after graduation	190 (58%)	—	—		—	—
<5 years after graduation	138 (42%)	0.8	-0.3, 1.9	0.151	0.8	-0.4, 2.0	0.189
Maternal age at conception (years)	330	-0.1	-0.2, 0.0	0.191	-0.1	-0.2, 0.1	0.488
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—
19-23.9 Kg/m2	208 (63%)	0.9	-0.8, 2.5	0.309	0.8	-0.8, 2.5	0.321
≥24 Kg/m2	75 (23%)	0.7	-1.2, 2.6	0.493	0.6	-1.3, 2.6	0.536
Child sex
Male	175 (53%)	—	—		—	—
Female	155 (47%)	-1.2	-2.3, 0.0	0.042	-0.7	-1.9, 0.5	0.237
Maternal parity
None	148 (45%)	—	—		—	—
1 child or more	182 (55%)	-1.0	-2.1, 0.1	0.083	-1.5	-2.7, -0.2	0.021
Breastfeeding duration
Not breastfed	24 (7.5%)	—	—		—	—
<24 weeks	114 (35%)	-0.3	-2.5, 2.0	0.813	0.1	-2.2, 2.4	0.936
24-47 weeks	109 (34%)	-0.3	-2.5, 2.0	0.829	0.6	-1.8, 3.0	0.627
Still breastfeed at 48 weeks	75 (23%)	0.4	-2.0, 2.7	0.760	1.1	-1.3, 3.5	0.382
Gestational duration, completed weeks	330	0.0	-0.4, 0.3	0.790	-0.1	-0.5, 0.3	0.690
Delivery mode
Vaginal delivery	276 (84%)	—	—		—	—
C-section	54 (16%)	0.5	-1.0, 2.0	0.505	0.0	-1.6, 1.7	0.958
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	236 (79%)	—	—		—	—
Between 6 and 12 months old	48 (16%)	0.1	-1.5, 1.7	0.933	-0.6	-2.3, 1.0	0.461
Not introduced at 12 months old	15 (5.0%)	2.2	-0.4, 4.9	0.102	1.8	-1.0, 4.6	0.205
Presence of pets
No	209 (72%)	—	—		—	—
One or more	83 (28%)	0.3	-1.0, 1.6	0.625	0.1	-1.3, 1.6	0.878
Antibiotics use between 0-12 months old
No	229 (70%)	—	—		—	—
Yes	100 (30%)	-0.2	-1.4, 1.0	0.793	0.0	-1.2, 1.3	0.958
HOME questionnaire total score	301	-0.1	-0.3, 0.1	0.442	-0.1	-0.3, 0.2	0.538
Maternal anxiety and depression score during the third trimester of pregnancy	320	0.1	0.0, 0.3	0.014	0.2	0.0, 0.3	0.017
Maternal active smoking during pregnancy	19 (6.2%)
No		—	—		—	—
Yes		0.5	-1.9, 2.9	0.680	-0.1	-2.7, 2.5	0.943
Child perinatal passive smoking up to one year	103 (32%)
No		—	—		—	—
Yes		0.5	-0.7, 1.7	0.411	0.3	-1.1, 1.7	0.667
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	255 (82%)	—	—		—	—
Other	57 (18%)	-0.6	-2.1, 0.9	0.449	-0.5	-2.1, 1.0	0.497
Child age at the SRS 3 years evaluation	330	0.1	0.0, 0.2	0.076
Child age at the SRS 3 years evaluation					0.1	0.0, 0.2	0.119
No. Obs.					330
R²					0.097
Adjusted R²					0.022
1 n (%); N
2 CI = Confidence Interval

Shift score Y3

Characteristic		Univariate models			Multivariate model
	N = 3381	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	70 (21%)	—	—		—	—
3-3.4 Kg	166 (49%)	0.2	-0.7, 1.0	0.703	-0.2	-1.2, 0.8	0.736
≥3.5 Kg	102 (30%)	0.6	-0.3, 1.5	0.218	0.3	-1.0, 1.6	0.629
Birth length
<50 cm	121 (36%)	—	—		—	—
50-51 cm	135 (40%)	0.4	-0.4, 1.1	0.312	0.2	-0.6, 1.1	0.583
≥52 cm	81 (24%)	0.3	-0.5, 1.2	0.420	0.3	-0.9, 1.4	0.656
Maternal education
≥5 years after graduation	195 (58%)	—	—		—	—
<5 years after graduation	141 (42%)	0.3	-0.4, 0.9	0.415	0.4	-0.3, 1.1	0.223
Maternal age at conception (years)	338	0.0	-0.1, 0.0	0.381	0.0	-0.1, 0.0	0.297
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—
19-23.9 Kg/m2	213 (63%)	-0.5	-1.5, 0.4	0.257	-0.3	-1.3, 0.6	0.492
≥24 Kg/m2	78 (23%)	-0.6	-1.7, 0.4	0.240	-0.6	-1.7, 0.5	0.251
Child sex
Male	181 (54%)	—	—		—	—
Female	157 (46%)	0.1	-0.5, 0.7	0.721	0.3	-0.4, 0.9	0.467
Maternal parity
None	154 (46%)	—	—		—	—
1 child or more	184 (54%)	-0.5	-1.2, 0.1	0.099	-0.8	-1.5, -0.1	0.023
Breastfeeding duration
Not breastfed	26 (7.9%)	—	—		—	—
<24 weeks	115 (35%)	0.4	-0.9, 1.7	0.546	0.7	-0.5, 2.0	0.266
24-47 weeks	112 (34%)	1.1	-0.2, 2.3	0.099	1.5	0.2, 2.8	0.021
Still breastfeed at 48 weeks	77 (23%)	0.9	-0.4, 2.2	0.185	1.1	-0.2, 2.5	0.094
Gestational duration, completed weeks	338	0.1	-0.1, 0.3	0.357	0.1	-0.2, 0.3	0.562
Delivery mode
Vaginal delivery	282 (83%)	—	—		—	—
C-section	56 (17%)	0.2	-0.6, 1.1	0.577	0.2	-0.7, 1.1	0.608
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	243 (79%)	—	—		—	—
Between 6 and 12 months old	49 (16%)	0.0	-0.9, 0.9	0.975	-0.6	-1.5, 0.3	0.205
Not introduced at 12 months old	15 (4.9%)	-0.1	-1.6, 1.4	0.902	0.0	-1.7, 1.7	0.998
Presence of pets
No	215 (72%)	—	—		—	—
One or more	84 (28%)	-0.2	-1.0, 0.5	0.562	-0.4	-1.3, 0.4	0.326
Antibiotics use between 0-12 months old
No	232 (69%)	—	—		—	—
Yes	105 (31%)	-0.1	-0.8, 0.6	0.756	-0.1	-0.8, 0.6	0.822
HOME questionnaire total score	309	0.0	-0.1, 0.1	0.688	0.0	-0.1, 0.1	0.983
Maternal anxiety and depression score during the third trimester of pregnancy	327	0.1	0.0, 0.2	0.014	0.1	0.0, 0.2	0.004
Maternal active smoking during pregnancy	19 (6.1%)
No		—	—		—	—
Yes		-0.6	-1.9, 0.7	0.348	-0.3	-2.7, 2.0	0.753
Child perinatal passive smoking up to one year	105 (32%)
No		—	—		—	—
Yes		0.0	-0.7, 0.7	0.996	-0.1	-0.9, 0.7	0.839
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	263 (82%)	—	—		—	—
Other	57 (18%)	0.9	0.0, 1.7	0.045	1.0	0.1, 1.9	0.027
Child age at the SRS 3 years evaluation	338	0.0	0.0, 0.1	0.324
Child age at the SRS 3 years evaluation					0.0	0.0, 0.1	0.308
No. Obs.					338
R²					0.098
Adjusted R²					0.026
1 n (%); N
2 CI = Confidence Interval

BRIEF-P emotional control score Y3

Characteristic		Univariate models			Multivariate model
	N = 3371	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	70 (21%)	—	—		—	—
3-3.4 Kg	165 (49%)	0.2	-0.8, 1.2	0.707	0.0	-1.2, 1.1	0.945
≥3.5 Kg	102 (30%)	0.4	-0.7, 1.4	0.506	0.2	-1.3, 1.7	0.817
Birth length
<50 cm	121 (36%)	—	—		—	—
50-51 cm	134 (40%)	0.3	-0.6, 1.1	0.525	0.2	-0.8, 1.2	0.706
≥52 cm	81 (24%)	0.4	-0.6, 1.3	0.463	0.3	-1.0, 1.7	0.632
Maternal education
≥5 years after graduation	194 (58%)	—	—		—	—
<5 years after graduation	141 (42%)	0.4	-0.4, 1.1	0.300	0.4	-0.4, 1.2	0.283
Maternal age at conception (years)	337	-0.1	-0.2, 0.0	0.048	-0.1	-0.2, 0.0	0.166
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—
19-23.9 Kg/m2	212 (63%)	0.5	-0.6, 1.6	0.381	0.7	-0.4, 1.8	0.211
≥24 Kg/m2	78 (23%)	0.2	-1.1, 1.5	0.746	0.3	-1.0, 1.6	0.699
Child sex
Male	180 (53%)	—	—		—	—
Female	157 (47%)	0.0	-0.8, 0.7	0.925	0.2	-0.6, 1.0	0.636
Maternal parity
None	153 (45%)	—	—		—	—
1 child or more	184 (55%)	-0.9	-1.6, -0.2	0.016	-1.2	-2.0, -0.3	0.007
Breastfeeding duration
Not breastfed	26 (7.9%)	—	—		—	—
<24 weeks	115 (35%)	-0.1	-1.6, 1.3	0.846	0.1	-1.4, 1.6	0.927
24-47 weeks	111 (34%)	0.5	-1.0, 2.0	0.493	1.0	-0.6, 2.5	0.217
Still breastfeed at 48 weeks	77 (23%)	0.7	-0.9, 2.2	0.379	1.0	-0.6, 2.6	0.218
Gestational duration, completed weeks	337	0.1	-0.1, 0.3	0.475	0.1	-0.2, 0.3	0.675
Delivery mode
Vaginal delivery	282 (84%)	—	—		—	—
C-section	55 (16%)	0.2	-0.8, 1.2	0.767	0.0	-1.0, 1.1	0.945
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	243 (79%)	—	—		—	—
Between 6 and 12 months old	48 (16%)	-0.1	-1.2, 0.9	0.786	-0.4	-1.6, 0.7	0.476
Not introduced at 12 months old	15 (4.9%)	1.1	-0.7, 2.9	0.236	1.3	-0.6, 3.2	0.175
Presence of pets
No	215 (72%)	—	—		—	—
One or more	84 (28%)	0.4	-0.4, 1.3	0.305	0.2	-0.8, 1.1	0.746
Antibiotics use between 0-12 months old
No	232 (69%)	—	—		—	—
Yes	104 (31%)	-0.1	-0.9, 0.7	0.835	0.1	-0.8, 0.9	0.849
HOME questionnaire total score	308	-0.1	-0.2, 0.1	0.440	0.0	-0.2, 0.1	0.633
Maternal anxiety and depression score during the third trimester of pregnancy	327	0.1	0.0, 0.2	0.037	0.1	0.0, 0.2	0.008
Maternal active smoking during pregnancy	19 (6.1%)
No		—	—		—	—
Yes		0.0	-1.6, 1.6	0.997	0.1	-2.0, 2.3	0.893
Child perinatal passive smoking up to one year	105 (32%)
No		—	—		—	—
Yes		0.3	-0.5, 1.1	0.455	0.1	-0.8, 0.9	0.850
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	262 (82%)	—	—		—	—
Other	57 (18%)	0.0	-1.0, 1.0	0.979	0.1	-0.9, 1.2	0.809
Child age at the SRS 3 years evaluation	337	0.0	-0.1, 0.1	0.923
Child age at the SRS 3 years evaluation					0.0	-0.1, 0.1	0.802
No. Obs.					337
R²					0.087
Adjusted R²					0.013
1 n (%); N
2 CI = Confidence Interval

BRIEF-P working memory score Y3

Characteristic		Univariate models			Multivariate model
	N = 3291	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	69 (21%)	—	—		—	—
3-3.4 Kg	162 (49%)	-1.0	-2.2, 0.2	0.114	-1.4	-2.9, 0.1	0.061
≥3.5 Kg	98 (30%)	-0.5	-1.8, 0.8	0.468	-0.7	-2.6, 1.1	0.437
Birth length
<50 cm	118 (36%)	—	—		—	—
50-51 cm	131 (40%)	-0.1	-1.2, 1.0	0.848	-0.2	-1.5, 1.0	0.720
≥52 cm	79 (24%)	-0.2	-1.4, 1.1	0.808	-0.5	-2.2, 1.2	0.568
Maternal education
≥5 years after graduation	192 (59%)	—	—		—	—
<5 years after graduation	135 (41%)	0.8	-0.1, 1.8	0.085	0.9	0.0, 1.9	0.061
Maternal age at conception (years)	329	0.0	-0.2, 0.1	0.553	0.0	-0.1, 0.1	0.865
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—
19-23.9 Kg/m2	207 (63%)	0.7	-0.7, 2.1	0.341	0.9	-0.5, 2.4	0.192
≥24 Kg/m2	76 (23%)	-0.3	-1.9, 1.3	0.705	-0.1	-1.7, 1.5	0.915
Child sex
Male	177 (54%)	—	—		—	—
Female	152 (46%)	-0.1	-1.0, 0.9	0.908	-0.2	-1.2, 0.8	0.738
Maternal parity
None	152 (46%)	—	—		—	—
1 child or more	177 (54%)	-1.2	-2.1, -0.3	0.012	-1.4	-2.4, -0.3	0.009
Breastfeeding duration
Not breastfed	25 (7.8%)	—	—		—	—
<24 weeks	113 (35%)	0.5	-1.5, 2.4	0.643	0.7	-1.2, 2.7	0.460
24-47 weeks	110 (34%)	0.5	-1.4, 2.5	0.580	1.3	-0.7, 3.2	0.203
Still breastfeed at 48 weeks	73 (23%)	0.5	-1.5, 2.5	0.626	1.2	-0.8, 3.2	0.232
Gestational duration, completed weeks	329	0.1	-0.2, 0.4	0.352	0.3	-0.1, 0.6	0.112
Delivery mode
Vaginal delivery	274 (83%)	—	—		—	—
C-section	55 (17%)	0.2	-1.1, 1.4	0.780	-0.2	-1.5, 1.1	0.781
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	235 (79%)	—	—		—	—
Between 6 and 12 months old	49 (16%)	-0.3	-1.7, 1.0	0.626	-0.9	-2.2, 0.4	0.171
Not introduced at 12 months old	14 (4.7%)	1.4	-0.9, 3.7	0.237	1.4	-1.2, 4.1	0.291
Presence of pets
No	208 (72%)	—	—		—	—
One or more	82 (28%)	-0.8	-1.8, 0.3	0.159	-0.9	-2.0, 0.2	0.128
Antibiotics use between 0-12 months old
No	224 (68%)	—	—		—	—
Yes	104 (32%)	0.2	-0.8, 1.2	0.728	0.4	-0.6, 1.5	0.418
HOME questionnaire total score	300	-0.2	-0.4, 0.0	0.062	-0.1	-0.3, 0.1	0.211
Maternal anxiety and depression score during the third trimester of pregnancy	318	0.1	0.0, 0.2	0.102	0.1	0.0, 0.2	0.015
Maternal active smoking during pregnancy	18 (5.9%)
No		—	—		—	—
Yes		0.6	-1.4, 2.6	0.556	-0.3	-2.6, 2.1	0.806
Child perinatal passive smoking up to one year	103 (32%)
No		—	—		—	—
Yes		1.2	0.2, 2.1	0.024	0.9	-0.4, 2.1	0.177
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	256 (82%)	—	—		—	—
Other	55 (18%)	-1.3	-2.6, 0.0	0.045	-0.8	-2.1, 0.6	0.263
Child age at the SRS 3 years evaluation	329	0.1	0.0, 0.2	0.234
Child age at the SRS 3 years evaluation					0.1	0.0, 0.2	0.232
No. Obs.					329
R²					0.124
Adjusted R²					0.052
1 n (%); N
2 CI = Confidence Interval

BRIEF-P plan/organization score Y3

Characteristic		Univariate models			Multivariate model
	N = 3351	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	70 (21%)	—	—		—	—
3-3.4 Kg	165 (49%)	-0.2	-0.9, 0.6	0.678	-0.3	-1.2, 0.6	0.536
≥3.5 Kg	100 (30%)	-0.1	-0.9, 0.8	0.893	-0.2	-1.4, 1.0	0.728
Birth length
<50 cm	121 (36%)	—	—		—	—
50-51 cm	135 (40%)	-0.1	-0.8, 0.6	0.745	-0.2	-1.1, 0.6	0.557
≥52 cm	78 (23%)	0.2	-0.6, 1.0	0.567	0.2	-0.9, 1.3	0.767
Maternal education
≥5 years after graduation	193 (58%)	—	—		—	—
<5 years after graduation	140 (42%)	0.8	0.2, 1.4	0.008	0.9	0.3, 1.6	0.003
Maternal age at conception (years)	335	0.0	-0.1, 0.0	0.209	0.0	-0.1, 0.1	0.470
Maternal BMI before pregnancy
<19 Kg/m2	46 (14%)	—	—		—	—
19-23.9 Kg/m2	212 (63%)	0.0	-0.9, 0.9	0.950	0.0	-0.9, 0.9	0.938
≥24 Kg/m2	76 (23%)	-0.2	-1.3, 0.8	0.663	-0.3	-1.3, 0.8	0.613
Child sex
Male	179 (53%)	—	—		—	—
Female	156 (47%)	-0.2	-0.8, 0.4	0.416	-0.2	-0.8, 0.5	0.558
Maternal parity
None	153 (46%)	—	—		—	—
1 child or more	182 (54%)	-0.5	-1.1, 0.1	0.086	-0.7	-1.3, 0.0	0.050
Breastfeeding duration
Not breastfed	26 (8.0%)	—	—		—	—
<24 weeks	114 (35%)	-0.4	-1.6, 0.8	0.509	-0.2	-1.4, 1.0	0.719
24-47 weeks	111 (34%)	0.2	-1.0, 1.3	0.797	0.6	-0.7, 1.9	0.369
Still breastfeed at 48 weeks	76 (23%)	-0.1	-1.4, 1.1	0.838	0.3	-1.0, 1.6	0.651
Gestational duration, completed weeks	335	0.0	-0.2, 0.2	0.841	0.1	-0.2, 0.3	0.603
Delivery mode
Vaginal delivery	281 (84%)	—	—		—	—
C-section	54 (16%)	0.1	-0.7, 1.0	0.733	-0.1	-1.0, 0.8	0.804
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	241 (79%)	—	—		—	—
Between 6 and 12 months old	49 (16%)	0.0	-0.9, 0.9	0.977	-0.4	-1.3, 0.5	0.351
Not introduced at 12 months old	15 (4.9%)	1.6	0.1, 3.0	0.037	1.6	0.1, 3.1	0.040
Presence of pets
No	213 (72%)	—	—		—	—
One or more	84 (28%)	-0.3	-1.0, 0.4	0.368	-0.5	-1.2, 0.2	0.184
Antibiotics use between 0-12 months old
No	232 (69%)	—	—		—	—
Yes	102 (31%)	0.1	-0.5, 0.8	0.727	0.2	-0.5, 0.8	0.614
HOME questionnaire total score	306	0.0	-0.1, 0.1	0.769	0.1	-0.1, 0.2	0.402
Maternal anxiety and depression score during the third trimester of pregnancy	324	0.1	0.0, 0.1	0.042	0.1	0.0, 0.2	0.013
Maternal active smoking during pregnancy	19 (6.1%)
No		—	—		—	—
Yes		-0.1	-1.4, 1.2	0.922	-0.4	-1.8, 0.9	0.539
Child perinatal passive smoking up to one year	103 (32%)
No		—	—		—	—
Yes		0.5	-0.2, 1.1	0.159	0.4	-0.3, 1.2	0.255
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	261 (82%)	—	—		—	—
Other	57 (18%)	-0.3	-1.1, 0.5	0.466	-0.2	-1.1, 0.6	0.592
Child age at the SRS 3 years evaluation	335	0.0	0.0, 0.1	0.208
Child age at the SRS 3 years evaluation					0.0	0.0, 0.1	0.311
No. Obs.					335
R²					0.107
Adjusted R²					0.035
1 n (%); N
2 CI = Confidence Interval

IQ Y3

IQ verbal comprehension score Y3

Characteristic		Univariate models			Multivariate model
	N = 3151	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	63 (20%)	—	—		—	—
3-3.4 Kg	159 (50%)	-0.7	-4.1, 2.7	0.697	1.9	-2.1, 5.9	0.357
≥3.5 Kg	93 (30%)	-0.9	-4.7, 2.8	0.619	2.1	-3.1, 7.3	0.421
Birth length
<50 cm	116 (37%)	—	—		—	—
50-51 cm	124 (39%)	-2.0	-4.9, 1.0	0.191	-2.1	-5.6, 1.4	0.249
≥52 cm	74 (24%)	-1.1	-4.5, 2.2	0.504	-0.4	-5.0, 4.2	0.868
Maternal education
≥5 years after graduation	182 (58%)	—	—		—	—
<5 years after graduation	131 (42%)	-2.1	-4.7, 0.5	0.105	-1.5	-4.2, 1.1	0.255
Maternal age at conception (years)	315	0.0	-0.4, 0.3	0.907	0.1	-0.3, 0.4	0.655
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—
19-23.9 Kg/m2	198 (63%)	0.7	-3.0, 4.5	0.709	0.8	-3.0, 4.6	0.678
≥24 Kg/m2	71 (23%)	0.9	-3.4, 5.2	0.690	1.1	-3.3, 5.5	0.621
Child sex
Male	167 (53%)	—	—		—	—
Female	148 (47%)	2.6	0.0, 5.1	0.046	1.5	-1.3, 4.2	0.293
Maternal parity
None	139 (44%)	—	—		—	—
1 child or more	176 (56%)	-3.3	-5.8, -0.7	0.012	-3.0	-5.8, -0.2	0.036
Breastfeeding duration
Not breastfed	25 (8.1%)	—	—		—	—
<24 weeks	102 (33%)	0.7	-4.3, 5.8	0.779	-0.7	-5.8, 4.5	0.802
24-47 weeks	108 (35%)	2.4	-2.7, 7.4	0.353	1.0	-4.1, 6.1	0.692
Still breastfeed at 48 weeks	72 (23%)	4.3	-1.0, 9.5	0.112	4.3	-1.1, 9.6	0.117
Gestational duration, completed weeks	315	-0.3	-1.2, 0.5	0.451	-0.4	-1.4, 0.6	0.418
Delivery mode
Vaginal delivery	263 (83%)	—	—		—	—
C-section	52 (17%)	-0.2	-3.7, 3.2	0.887	-1.2	-4.8, 2.4	0.507
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	232 (80%)	—	—		—	—
Between 6 and 12 months old	45 (16%)	1.0	-2.7, 4.7	0.593	1.3	-2.7, 5.3	0.514
Not introduced at 12 months old	13 (4.5%)	-7.6	-14.0, -1.2	0.021	-6.0	-12.5, 0.5	0.069
Presence of pets
No	203 (73%)	—	—		—	—
One or more	77 (28%)	0.3	-2.7, 3.3	0.850	0.5	-2.8, 3.7	0.779
Antibiotics use between 0-12 months old
No	212 (68%)	—	—		—	—
Yes	102 (32%)	-0.8	-3.6, 1.9	0.546	-0.7	-3.5, 2.1	0.631
HOME questionnaire total score	309	0.8	0.3, 1.2	0.002	0.6	0.1, 1.1	0.021
Maternal anxiety and depression score during the third trimester of pregnancy	306	-0.2	-0.5, 0.1	0.176	-0.1	-0.4, 0.2	0.335
Maternal active smoking during pregnancy	19 (6.5%)
No		—	—		—	—
Yes		-0.7	-6.1, 4.8	0.807	1.3	-4.9, 7.5	0.681
Child perinatal passive smoking up to one year	100 (33%)
No		—	—		—	—
Yes		-1.2	-3.9, 1.6	0.407	-0.5	-3.5, 2.6	0.763
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	246 (82%)	—	—		—	—
Other	53 (18%)	-3.0	-6.4, 0.4	0.081	-2.6	-6.3, 1.1	0.166
Child age at the IQ 3 years evaluation	315	0.3	0.0, 0.6	0.065
Child age at the IQ 3 years evaluation					0.3	0.0, 0.6	0.082
No. Obs.					315
R²					0.124
Adjusted R²					0.048
1 n (%); N
2 CI = Confidence Interval

IQ visuospacial score Y3

Characteristic		Univariate models			Multivariate model
	N = 3151	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	63 (20%)	—	—		—	—
3-3.4 Kg	159 (50%)	1.3	-2.0, 4.5	0.452	0.6	-3.4, 4.6	0.786
≥3.5 Kg	93 (30%)	0.9	-2.7, 4.5	0.611	0.0	-5.1, 5.1	0.990
Birth length
<50 cm	116 (37%)	—	—		—	—
50-51 cm	124 (39%)	0.9	-1.9, 3.8	0.511	0.4	-3.0, 3.9	0.808
≥52 cm	74 (24%)	0.3	-2.9, 3.6	0.839	0.3	-4.2, 4.9	0.883
Maternal education
≥5 years after graduation	182 (58%)	—	—		—	—
<5 years after graduation	131 (42%)	0.6	-1.9, 3.1	0.630	1.2	-1.4, 3.8	0.363
Maternal age at conception (years)	315	0.2	-0.2, 0.5	0.349	0.1	-0.3, 0.4	0.649
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—
19-23.9 Kg/m2	198 (63%)	0.9	-2.7, 4.5	0.622	0.5	-3.2, 4.3	0.772
≥24 Kg/m2	71 (23%)	1.7	-2.5, 5.9	0.429	1.6	-2.7, 6.0	0.464
Child sex
Male	167 (53%)	—	—		—	—
Female	148 (47%)	0.5	-2.0, 2.9	0.708	0.1	-2.6, 2.9	0.934
Maternal parity
None	139 (44%)	—	—		—	—
1 child or more	176 (56%)	2.6	0.1, 5.0	0.041	2.4	-0.4, 5.2	0.089
Breastfeeding duration
Not breastfed	25 (8.1%)	—	—		—	—
<24 weeks	102 (33%)	3.6	-1.2, 8.4	0.138	3.3	-1.7, 8.3	0.200
24-47 weeks	108 (35%)	5.3	0.5, 10.0	0.030	5.1	0.0, 10.1	0.048
Still breastfeed at 48 weeks	72 (23%)	6.1	1.1, 11.1	0.016	6.7	1.5, 11.9	0.011
Gestational duration, completed weeks	315	0.0	-0.8, 0.8	0.948	0.0	-1.0, 1.0	0.982
Delivery mode
Vaginal delivery	263 (83%)	—	—		—	—
C-section	52 (17%)	-2.3	-5.6, 1.1	0.182	-2.4	-6.0, 1.1	0.176
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	232 (80%)	—	—		—	—
Between 6 and 12 months old	45 (16%)	-0.8	-4.4, 2.9	0.672	-0.4	-3.8, 3.1	0.840
Not introduced at 12 months old	13 (4.5%)	-3.0	-9.3, 3.4	0.357	-2.2	-8.8, 4.3	0.501
Presence of pets
No	203 (73%)	—	—		—	—
One or more	77 (28%)	-1.4	-4.4, 1.5	0.339	-1.6	-4.7, 1.4	0.297
Antibiotics use between 0-12 months old
No	212 (68%)	—	—		—	—
Yes	102 (32%)	1.6	-1.0, 4.2	0.225	1.7	-1.2, 4.5	0.248
HOME questionnaire total score	309	0.3	-0.2, 0.7	0.274	0.4	-0.2, 0.9	0.171
Maternal anxiety and depression score during the third trimester of pregnancy	306	-0.1	-0.3, 0.2	0.707	0.0	-0.3, 0.3	0.853
Maternal active smoking during pregnancy	19 (6.5%)
No		—	—		—	—
Yes		-2.0	-7.2, 3.2	0.453	-1.6	-7.0, 3.7	0.552
Child perinatal passive smoking up to one year	100 (33%)
No		—	—		—	—
Yes		-0.9	-3.6, 1.8	0.522	-0.6	-3.5, 2.3	0.678
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	246 (82%)	—	—		—	—
Other	53 (18%)	-1.8	-5.2, 1.5	0.286	-3.4	-6.9, 0.1	0.058
Child age at the IQ 3 years evaluation	315	0.0	-0.3, 0.3	0.862
Child age at the IQ 3 years evaluation					0.0	-0.3, 0.3	0.939
No. Obs.					315
R²					0.078
Adjusted R²
1 n (%); N
2 CI = Confidence Interval

IQ work memory score Y3

Characteristic		Univariate models			Multivariate model
	N = 3151	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	63 (20%)	—	—		—	—
3-3.4 Kg	159 (50%)	0.8	-2.4, 4.1	0.610	0.3	-3.6, 4.3	0.875
≥3.5 Kg	93 (30%)	-1.4	-4.9, 2.1	0.441	-2.2	-7.2, 2.8	0.390
Birth length
<50 cm	116 (37%)	—	—		—	—
50-51 cm	124 (39%)	0.0	-2.9, 2.8	0.973	0.3	-3.1, 3.7	0.846
≥52 cm	74 (24%)	-1.3	-4.6, 1.9	0.415	0.0	-4.5, 4.5	0.998
Maternal education
≥5 years after graduation	182 (58%)	—	—		—	—
<5 years after graduation	131 (42%)	0.0	-2.5, 2.5	0.974	0.2	-2.4, 2.8	0.886
Maternal age at conception (years)	315	-0.1	-0.5, 0.2	0.362	-0.2	-0.6, 0.1	0.239
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—
19-23.9 Kg/m2	198 (63%)	-2.1	-5.7, 1.4	0.240	-3.0	-6.7, 0.7	0.111
≥24 Kg/m2	71 (23%)	-1.1	-5.2, 3.0	0.597	-1.6	-5.8, 2.7	0.477
Child sex
Male	167 (53%)	—	—		—	—
Female	148 (47%)	1.7	-0.7, 4.2	0.169	1.3	-1.4, 4.0	0.353
Maternal parity
None	139 (44%)	—	—		—	—
1 child or more	176 (56%)	1.7	-0.7, 4.2	0.167	2.9	0.2, 5.7	0.036
Breastfeeding duration
Not breastfed	25 (8.1%)	—	—		—	—
<24 weeks	102 (33%)	0.7	-4.1, 5.5	0.779	0.8	-4.3, 5.8	0.767
24-47 weeks	108 (35%)	0.1	-4.7, 4.9	0.970	-0.6	-5.6, 4.3	0.804
Still breastfeed at 48 weeks	72 (23%)	4.0	-1.0, 9.0	0.117	4.2	-1.0, 9.3	0.112
Gestational duration, completed weeks	315	0.0	-0.8, 0.8	0.970	0.2	-0.8, 1.1	0.731
Delivery mode
Vaginal delivery	263 (83%)	—	—		—	—
C-section	52 (17%)	-1.3	-4.6, 2.0	0.447	-0.5	-3.9, 3.0	0.795
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	232 (80%)	—	—		—	—
Between 6 and 12 months old	45 (16%)	-1.7	-5.2, 1.8	0.349	-0.5	-4.0, 3.0	0.775
Not introduced at 12 months old	13 (4.5%)	-4.2	-10.3, 1.9	0.176	-3.7	-10.3, 2.9	0.269
Presence of pets
No	203 (73%)	—	—		—	—
One or more	77 (28%)	-0.8	-3.7, 2.1	0.600	-0.7	-3.8, 2.3	0.636
Antibiotics use between 0-12 months old
No	212 (68%)	—	—		—	—
Yes	102 (32%)	0.9	-1.7, 3.5	0.506	1.0	-1.8, 3.8	0.469
HOME questionnaire total score	309	0.2	-0.2, 0.7	0.328	0.3	-0.2, 0.8	0.220
Maternal anxiety and depression score during the third trimester of pregnancy	306	-0.1	-0.4, 0.1	0.279	-0.1	-0.4, 0.2	0.360
Maternal active smoking during pregnancy	19 (6.5%)
No		—	—		—	—
Yes		-4.8	-9.9, 0.3	0.062	-3.8	-9.3, 1.6	0.166
Child perinatal passive smoking up to one year	100 (33%)
No		—	—		—	—
Yes		-1.0	-3.6, 1.7	0.468	0.2	-2.7, 3.1	0.910
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	246 (82%)	—	—		—	—
Other	53 (18%)	-1.6	-4.9, 1.6	0.326	-2.8	-6.3, 0.7	0.117
Child age at the IQ 3 years evaluation	315	0.1	-0.2, 0.4	0.493
Child age at the IQ 3 years evaluation					0.1	-0.2, 0.4	0.665
No. Obs.					315
R²					0.088
Adjusted R²					0.008
1 n (%); N
2 CI = Confidence Interval

IQ total score Y3

Characteristic		Univariate models			Multivariate model
	N = 3151	Beta	95% CI2	p-value	Beta	95% CI2	p-value
Birth weight
<3 Kg	63 (20%)	—	—		—	—
3-3.4 Kg	159 (50%)	0.5	-2.8, 3.8	0.781	1.2	-2.8, 5.2	0.552
≥3.5 Kg	93 (30%)	-0.3	-4.0, 3.3	0.854	0.3	-4.8, 5.5	0.896
Birth length
<50 cm	116 (37%)	—	—		—	—
50-51 cm	124 (39%)	-0.3	-3.1, 2.6	0.858	-0.2	-3.7, 3.2	0.888
≥52 cm	74 (24%)	-0.6	-3.9, 2.7	0.731	0.4	-4.2, 5.0	0.861
Maternal education
≥5 years after graduation	182 (58%)	—	—		—	—
<5 years after graduation	131 (42%)	-0.1	-2.6, 2.5	0.951	0.7	-2.0, 3.3	0.606
Maternal age at conception (years)	315	0.0	-0.3, 0.4	0.805	0.0	-0.3, 0.4	0.829
Maternal BMI before pregnancy
<19 Kg/m2	45 (14%)	—	—		—	—
19-23.9 Kg/m2	198 (63%)	0.5	-3.1, 4.2	0.779	0.0	-3.7, 3.8	0.991
≥24 Kg/m2	71 (23%)	1.3	-3.0, 5.5	0.560	1.0	-3.3, 5.4	0.643
Child sex
Male	167 (53%)	—	—		—	—
Female	148 (47%)	2.1	-0.4, 4.6	0.099	1.4	-1.4, 4.1	0.319
Maternal parity
None	139 (44%)	—	—		—	—
1 child or more	176 (56%)	0.3	-2.2, 2.8	0.799	0.8	-2.0, 3.6	0.583
Breastfeeding duration
Not breastfed	25 (8.1%)	—	—		—	—
<24 weeks	102 (33%)	2.3	-2.6, 7.3	0.358	1.6	-3.4, 6.7	0.526
24-47 weeks	108 (35%)	3.8	-1.1, 8.7	0.129	3.0	-2.0, 8.1	0.235
Still breastfeed at 48 weeks	72 (23%)	5.9	0.7, 11.0	0.026	6.3	1.1, 11.6	0.018
Gestational duration, completed weeks	315	-0.2	-1.0, 0.7	0.703	-0.2	-1.2, 0.8	0.661
Delivery mode
Vaginal delivery	263 (83%)	—	—		—	—
C-section	52 (17%)	-1.6	-5.0, 1.7	0.343	-1.8	-5.3, 1.7	0.316
Period of introduction of solid food 0-12 months old
Between 0 and 6 months old	232 (80%)	—	—		—	—
Between 6 and 12 months old	45 (16%)	-0.4	-4.0, 3.2	0.845	0.3	-3.3, 4.0	0.861
Not introduced at 12 months old	13 (4.5%)	-6.9	-13.2, -0.6	0.031	-5.4	-12.2, 1.4	0.120
Presence of pets
No	203 (73%)	—	—		—	—
One or more	77 (28%)	-0.9	-3.8, 2.1	0.566	-0.8	-4.0, 2.3	0.597
Antibiotics use between 0-12 months old
No	212 (68%)	—	—		—	—
Yes	102 (32%)	0.5	-2.1, 3.2	0.691	0.7	-2.1, 3.5	0.637
HOME questionnaire total score	309	0.6	0.2, 1.1	0.009	0.6	0.1, 1.1	0.017
Maternal anxiety and depression score during the third trimester of pregnancy	306	-0.2	-0.5, 0.1	0.187	-0.1	-0.5, 0.2	0.364
Maternal active smoking during pregnancy	19 (6.5%)
No		—	—		—	—
Yes		-3.0	-8.3, 2.2	0.257	-1.8	-7.2, 3.6	0.522
Child perinatal passive smoking up to one year	100 (33%)
No		—	—		—	—
Yes		-1.3	-4.0, 1.5	0.362	-0.5	-3.4, 2.4	0.731
Main mode of child care at 12 months (2 categories, optimized 2)
Collective day care	246 (82%)	—	—		—	—
Other	53 (18%)	-3.1	-6.5, 0.2	0.068	-4.2	-7.8, -0.7	0.020
Child age at the IQ 3 years evaluation	315	0.1	-0.1, 0.4	0.323
Child age at the IQ 3 years evaluation					0.1	-0.2, 0.4	0.499
No. Obs.					315
R²					0.099
Adjusted R²					0.020
1 n (%); N
2 CI = Confidence Interval

Sensitivity analyses - rarefaction threshold

CBCL Y2

Interne score Y2

Characteristic	Child CBCL interne score at 2 years
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	332	0.01	-0.01, 0.03	0.536
Specific richness (threshold 5000 reads, n=339)	321	0.01	-0.01, 0.03	0.485
Specific richness (threshold 10000 reads, n=339)	321	0.01	-0.01, 0.03	0.237
Shannon diversity (threshold 5000 reads, n=350, main analysis)	332	0.38	-0.56, 1.33	0.424
Shannon diversity (threshold 5000 reads, n=339)	321	0.46	-0.50, 1.41	0.348
Shannon diversity (threshold 10000 reads, n=339)	321	0.46	-0.49, 1.42	0.343
1 CI = Confidence Interval

Externe score Y2

Characteristic	Child CBCL externe score at 2 years
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	331	-0.01	-0.03, 0.02	0.629
Specific richness (threshold 5000 reads, n=339)	320	-0.01	-0.03, 0.02	0.611
Specific richness (threshold 10000 reads, n=339)	320	0.00	-0.02, 0.02	0.908
Shannon diversity (threshold 5000 reads, n=350, main analysis)	331	0.50	-0.76, 1.75	0.436
Shannon diversity (threshold 5000 reads, n=339)	320	0.47	-0.82, 1.75	0.475
Shannon diversity (threshold 10000 reads, n=339)	320	0.47	-0.81, 1.75	0.470
1 CI = Confidence Interval

SRS total score 3Y

Characteristic	Child SRS total score at 3 years
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	327	0.02	-0.04, 0.07	0.570
Specific richness (threshold 5000 reads, n=339)	316	0.02	-0.04, 0.07	0.512
Specific richness (threshold 10000 reads, n=339)	316	0.01	-0.03, 0.06	0.549
Shannon diversity (threshold 5000 reads, n=350, main analysis)	327	-0.10	-2.58, 2.38	0.938
Shannon diversity (threshold 5000 reads, n=339)	316	0.05	-2.47, 2.57	0.968
Shannon diversity (threshold 10000 reads, n=339)	316	0.05	-2.47, 2.57	0.970
1 CI = Confidence Interval

BRIEF-P Y3

Inhibit score Y3

Characteristic	Child inhibition score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	325	0.00	-0.02, 0.03	0.711
Specific richness (threshold 5000 reads, n=339)	314	0.01	-0.02, 0.03	0.637
Specific richness (threshold 10000 reads, n=339)	314	0.00	-0.02, 0.02	0.813
Shannon diversity (threshold 5000 reads, n=350, main analysis)	325	0.07	-0.97, 1.11	0.894
Shannon diversity (threshold 5000 reads, n=339)	314	0.22	-0.84, 1.28	0.687
Shannon diversity (threshold 10000 reads, n=339)	314	0.21	-0.85, 1.27	0.693
1 CI = Confidence Interval

Shift score Y3

Characteristic	Child shift score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	333	0.00	-0.01, 0.01	0.766
Specific richness (threshold 5000 reads, n=339)	322	0.00	-0.01, 0.01	0.729
Specific richness (threshold 10000 reads, n=339)	322	0.00	-0.01, 0.01	0.531
Shannon diversity (threshold 5000 reads, n=350, main analysis)	333	-0.16	-0.75, 0.42	0.587
Shannon diversity (threshold 5000 reads, n=339)	322	-0.08	-0.68, 0.51	0.783
Shannon diversity (threshold 10000 reads, n=339)	322	-0.08	-0.67, 0.51	0.784
1 CI = Confidence Interval

BRIEF-P emotional control score Y3

Characteristic	Child emotional control score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	332	0.01	0.00, 0.03	0.090
Specific richness (threshold 5000 reads, n=339)	321	0.01	0.00, 0.03	0.082
Specific richness (threshold 10000 reads, n=339)	321	0.01	0.00, 0.02	0.109
Shannon diversity (threshold 5000 reads, n=350, main analysis)	332	0.53	-0.16, 1.22	0.130
Shannon diversity (threshold 5000 reads, n=339)	321	0.59	-0.11, 1.28	0.097
Shannon diversity (threshold 10000 reads, n=339)	321	0.59	-0.11, 1.28	0.097
1 CI = Confidence Interval

BRIEF-P working memory score Y3

Characteristic	Child working memory score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	324	0.01	-0.01, 0.03	0.430
Specific richness (threshold 5000 reads, n=339)	315	0.01	-0.01, 0.03	0.409
Specific richness (threshold 10000 reads, n=339)	315	0.00	-0.01, 0.02	0.532
Shannon diversity (threshold 5000 reads, n=350, main analysis)	324	0.05	-0.83, 0.92	0.915
Shannon diversity (threshold 5000 reads, n=339)	315	0.09	-0.79, 0.98	0.839
Shannon diversity (threshold 10000 reads, n=339)	315	0.09	-0.79, 0.97	0.843
1 CI = Confidence Interval

BRIEF-P plan/organization score Y3

Characteristic	Child plan/organization score at 3 years (BRIEF-P)
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	330	0.01	0.00, 0.02	0.149
Specific richness (threshold 5000 reads, n=339)	319	0.01	0.00, 0.02	0.104
Specific richness (threshold 10000 reads, n=339)	319	0.01	0.00, 0.02	0.135
Shannon diversity (threshold 5000 reads, n=350, main analysis)	330	0.19	-0.37, 0.74	0.508
Shannon diversity (threshold 5000 reads, n=339)	319	0.20	-0.35, 0.76	0.469
Shannon diversity (threshold 10000 reads, n=339)	319	0.20	-0.35, 0.76	0.470
1 CI = Confidence Interval

IQ Y3

IQ verbal comprehension score Y3

Characteristic	Child verbal comprehension score at 3 years (IQ test)
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	310	-0.01	-0.06, 0.04	0.690
Specific richness (threshold 5000 reads, n=339)	301	-0.01	-0.06, 0.04	0.663
Specific richness (threshold 10000 reads, n=339)	301	-0.01	-0.05, 0.03	0.675
Shannon diversity (threshold 5000 reads, n=350, main analysis)	310	-1.28	-3.66, 1.10	0.290
Shannon diversity (threshold 5000 reads, n=339)	301	-1.18	-3.59, 1.23	0.336
Shannon diversity (threshold 10000 reads, n=339)	301	-1.19	-3.59, 1.22	0.333
1 CI = Confidence Interval

IQ visuospacial score Y3

Characteristic	Child visuospatiale score at 3 years (IQ test)
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	310	0.00	-0.05, 0.05	0.922
Specific richness (threshold 5000 reads, n=339)	301	0.00	-0.05, 0.04	0.867
Specific richness (threshold 10000 reads, n=339)	301	0.00	-0.04, 0.04	0.973
Shannon diversity (threshold 5000 reads, n=350, main analysis)	310	0.35	-1.99, 2.69	0.768
Shannon diversity (threshold 5000 reads, n=339)	301	0.24	-2.09, 2.58	0.837
Shannon diversity (threshold 10000 reads, n=339)	301	0.25	-2.08, 2.57	0.835
1 CI = Confidence Interval

IQ work memory score Y3

Characteristic	Child work memory score at 3 years (IQ test)
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	310	-0.01	-0.05, 0.04	0.800
Specific richness (threshold 5000 reads, n=339)	301	-0.01	-0.05, 0.04	0.827
Specific richness (threshold 10000 reads, n=339)	301	0.00	-0.04, 0.04	0.902
Shannon diversity (threshold 5000 reads, n=350, main analysis)	310	-1.04	-3.34, 1.25	0.372
Shannon diversity (threshold 5000 reads, n=339)	301	-1.08	-3.36, 1.20	0.352
Shannon diversity (threshold 10000 reads, n=339)	301	-1.07	-3.35, 1.20	0.353
1 CI = Confidence Interval

IQ total score Y3

Characteristic	Child total IQ score at 3 years
	N	Beta	95% CI1	p-value
Specific richness (threshold 5000 reads, n=350, main analysis)	310	0.00	-0.05, 0.05	0.997
Specific richness (threshold 5000 reads, n=339)	301	0.00	-0.05, 0.05	0.949
Specific richness (threshold 10000 reads, n=339)	301	0.00	-0.04, 0.04	0.998
Shannon diversity (threshold 5000 reads, n=350, main analysis)	310	-0.64	-3.00, 1.71	0.590
Shannon diversity (threshold 5000 reads, n=339)	301	-0.67	-3.02, 1.69	0.578
Shannon diversity (threshold 10000 reads, n=339)	301	-0.67	-3.02, 1.68	0.576
1 CI = Confidence Interval

Sensitivity analysis - effect of HOME variable

CBCL Y2

Interne score Y2

Characteristic	Child CBCL interne score at 2 years adjusted for HOME variable at 3 years (main analysis)				Child CBCL interne score at 2 years not adjusted for HOME variable at 3 years
	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value
Specific richness	332	0.01	-0.01, 0.03	0.536	332	0.01	-0.01, 0.03	0.437
Shannon diversity	332	0.38	-0.56, 1.33	0.424	332	0.45	-0.49, 1.39	0.348
Phylum Firmicutes	336	0.00	-0.03, 0.02	0.842	336	0.00	-0.03, 0.02	0.952
Phylum Actinobacteria	336	0.02	-0.01, 0.04	0.151	336	0.02	-0.01, 0.04	0.168
Phylum Bacteroidetes	336	0.00	-0.03, 0.03	0.869	336	0.00	-0.03, 0.03	0.836
Phylum Proteobacteria	336	-0.03	-0.06, 0.00	0.080	336	-0.03	-0.06, 0.00	0.068
Genus Bifidobacterium	336	0.02	-0.01, 0.04	0.134	336	0.02	-0.01, 0.04	0.151
Genus Bacteroides	336	-0.02	-0.05, 0.02	0.323	336	-0.02	-0.05, 0.01	0.302
Genus Blautia	336	-0.04	-0.09, 0.01	0.131	336	-0.04	-0.09, 0.02	0.177
Genera Escherichia and Shigella	336	-0.02	-0.06, 0.01	0.210	336	-0.03	-0.06, 0.01	0.172
1 CI = Confidence Interval

Externe score Y2

Characteristic	Child CBCL externe score at 2 years adjusted for HOME variable at 3 years (main analysis)				Child CBCL externe score at 2 years not adjusted for HOME variable at 3 years
	N	Beta	95% CI1	p-value	N	Beta	95% CI1	p-value
Specific richness	331	-0.01	-0.03, 0.02	0.629	331	0.00	-0.03, 0.02	0.786
Shannon diversity	331	0.50	-0.76, 1.75	0.436	331	0.61	-0.65, 1.86	0.341
Phylum Firmicutes	335	0.02	-0.01, 0.06	0.156	335	0.03	-0.01, 0.06	0.114
Phylum Actinobacteria	335	0.02	-0.01, 0.05	0.232	335	0.02	-0.01, 0.05	0.266
Phylum Bacteroidetes	335	-0.01	-0.05, 0.03	0.547	335	-0.01	-0.05, 0.03	0.520
Phylum Proteobacteria	335	-0.05	-0.10, -0.01	0.024	335	-0.05	-0.10, -0.01	0.019
Genus Bifidobacterium	335	0.02	-0.01, 0.05	0.203	335	0.02	-0.01, 0.05	0.237
Genus Bacteroides	335	-0.02	-0.06, 0.02	0.396	335	-0.02	-0.06, 0.02	0.374
Genus Blautia	335	0.03	-0.04, 0.10	0.377	335	0.04	-0.03, 0.11	0.287
Genera Escherichia and Shigella	335	-0.04	-0.09, 0.01	0.158	335	-0.04	-0.09, 0.01	0.119
1 CI = Confidence Interval